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- PDB-6igc: Crystal structure of HPV58/33/52 chimeric L1 pentamer -

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基本情報

登録情報
データベース: PDB / ID: 6igc
タイトルCrystal structure of HPV58/33/52 chimeric L1 pentamer
要素Major capsid protein L1
キーワードSTRUCTURAL PROTEIN / capsid protein
機能・相同性
機能・相同性情報


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
類似検索 - 分子機能
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
類似検索 - ドメイン・相同性
Major capsid protein L1
類似検索 - 構成要素
生物種Human papillomavirus type 58 (パピローマウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者Li, Z.H. / Song, S. / He, M.Z. / Gu, Y. / Li, S.W.
資金援助 中国, 6件
組織認可番号国
National Natural Science Foundation of China81701637 中国
National Science Foundation (China)81701637 中国
National Natural Science Foundation of ChinaU1705283 中国
National Science Foundation (China)U1705283 中国
National Natural Science Foundation of China31670935 中国
National Science Foundation (China)31670935 中国
引用ジャーナル: Nat Commun / 年: 2018
タイトル: Rational design of a triple-type human papillomavirus vaccine by compromising viral-type specificity.
著者: Zhihai Li / Shuo Song / Maozhou He / Daning Wang / Jingjie Shi / Xinlin Liu / Yunbing Li / Xin Chi / Shuangping Wei / Yurou Yang / Zhiping Wang / Jinjin Li / Huilian Qian / Hai Yu / Qingbing ...著者: Zhihai Li / Shuo Song / Maozhou He / Daning Wang / Jingjie Shi / Xinlin Liu / Yunbing Li / Xin Chi / Shuangping Wei / Yurou Yang / Zhiping Wang / Jinjin Li / Huilian Qian / Hai Yu / Qingbing Zheng / Xiaodong Yan / Qinjian Zhao / Jun Zhang / Ying Gu / Shaowei Li / Ningshao Xia /
要旨: Sequence variability in surface-antigenic sites of pathogenic proteins is an important obstacle in vaccine development. Over 200 distinct genomic sequences have been identified for human ...Sequence variability in surface-antigenic sites of pathogenic proteins is an important obstacle in vaccine development. Over 200 distinct genomic sequences have been identified for human papillomavirus (HPV), of which more than 18 are associated with cervical cancer. Here, based on the high structural similarity of L1 surface loops within a group of phylogenetically close HPV types, we design a triple-type chimera of HPV33/58/52 using loop swapping. The chimeric VLPs elicit neutralization titers comparable with a mix of the three wild-type VLPs both in mice and non-human primates. This engineered region of the chimeric protein recapitulates the conformational contours of the antigenic surfaces of the parental-type proteins, offering a basis for this high immunity. Our stratagem is equally successful in developing other triplet-type chimeras (HPV16/35/31, HPV56/66/53, HPV39/68/70, HPV18/45/59), paving the way for the development of an improved HPV prophylactic vaccine against all carcinogenic HPV strains. This technique may also be extrapolated to other microbes.
履歴
登録2018年9月25日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年11月21日Provider: repository / タイプ: Initial release
改定 1.12019年1月2日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
O: Major capsid protein L1
P: Major capsid protein L1
Q: Major capsid protein L1
R: Major capsid protein L1
S: Major capsid protein L1
T: Major capsid protein L1
U: Major capsid protein L1
V: Major capsid protein L1
W: Major capsid protein L1
X: Major capsid protein L1
Y: Major capsid protein L1
Z: Major capsid protein L1
a: Major capsid protein L1
b: Major capsid protein L1
c: Major capsid protein L1
d: Major capsid protein L1
e: Major capsid protein L1
f: Major capsid protein L1
g: Major capsid protein L1
h: Major capsid protein L1
i: Major capsid protein L1
j: Major capsid protein L1
k: Major capsid protein L1
l: Major capsid protein L1
m: Major capsid protein L1
n: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)2,365,77240
ポリマ－2,365,77240
非ポリマー00
水00
1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36010 Å2
ΔGint-209 kcal/mol
Surface area75370 Å2
手法PISA
2
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36380 Å2
ΔGint-205 kcal/mol
Surface area75050 Å2
手法PISA
3
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
O: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36250 Å2
ΔGint-208 kcal/mol
Surface area74690 Å2
手法PISA
4
P: Major capsid protein L1
Q: Major capsid protein L1
R: Major capsid protein L1
S: Major capsid protein L1
T: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36270 Å2
ΔGint-212 kcal/mol
Surface area75090 Å2
手法PISA
5
U: Major capsid protein L1
V: Major capsid protein L1
W: Major capsid protein L1
X: Major capsid protein L1
Y: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36220 Å2
ΔGint-209 kcal/mol
Surface area74420 Å2
手法PISA
6
Z: Major capsid protein L1
a: Major capsid protein L1
b: Major capsid protein L1
c: Major capsid protein L1
d: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36540 Å2
ΔGint-207 kcal/mol
Surface area74620 Å2
手法PISA
7
e: Major capsid protein L1
f: Major capsid protein L1
g: Major capsid protein L1
h: Major capsid protein L1
i: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35030 Å2
ΔGint-197 kcal/mol
Surface area76240 Å2
手法PISA
8
j: Major capsid protein L1
k: Major capsid protein L1
l: Major capsid protein L1
m: Major capsid protein L1
n: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)295,7225
ポリマ－295,7225
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36070 Å2
ΔGint-209 kcal/mol
Surface area75550 Å2
手法PISA
単位格子
Length a, b, c (Å)136.543, 209.761, 212.630
Angle α, β, γ (deg.)60.500, 85.070, 90.120
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 22 through 54 or resid 61...
21(chain B and (resid 22 through 54 or resid 61...
31(chain C and (resid 22 through 54 or resid 61...
41(chain D and (resid 22 through 54 or resid 61...
51(chain E and (resid 22 through 157 or resid 159 through 175 or resid 183 through 473))
61(chain F and (resid 22 through 54 or resid 61...
71(chain G and (resid 22 through 54 or resid 61...
81(chain H and (resid 22 through 54 or resid 61...
91(chain I and (resid 22 through 54 or resid 61...
101(chain J and (resid 22 through 54 or resid 61...
111(chain K and (resid 22 through 54 or resid 61...
121(chain L and (resid 22 through 54 or resid 61...
131(chain M and (resid 22 through 54 or resid 61...
141(chain N and (resid 22 through 54 or resid 61...
151(chain O and (resid 22 through 54 or resid 61...
161(chain P and (resid 22 through 54 or resid 61...
171(chain Q and (resid 22 through 54 or resid 61...
181(chain R and (resid 22 through 54 or resid 61...
191(chain S and (resid 22 through 54 or resid 61...
201(chain T and (resid 22 through 54 or resid 61...
211(chain U and (resid 22 through 54 or resid 61...
221(chain V and (resid 22 through 54 or resid 61...
231(chain W and (resid 22 through 54 or resid 61...
241(chain X and (resid 22 through 54 or resid 61...
251(chain Y and (resid 22 through 54 or resid 61...
261(chain Z and (resid 22 through 54 or resid 61...
271(chain a and (resid 22 through 54 or resid 61...
281(chain b and (resid 22 through 54 or resid 61...
291(chain c and (resid 22 through 54 or resid 61...
301(chain d and (resid 22 through 54 or resid 61...
311(chain e and (resid 22 through 54 or resid 61...
321(chain f and (resid 22 through 54 or resid 61...
331(chain g and (resid 22 through 54 or resid 61...
341(chain h and (resid 22 through 54 or resid 61...
351(chain i and (resid 22 through 54 or resid 61...
361(chain j and (resid 22 through 54 or resid 61...
371(chain k and (resid 22 through 54 or resid 61...
381(chain l and (resid 22 through 54 or resid 61...
391(chain m and (resid 22 through 54 or resid 61...
401(chain n and (resid 22 through 54 or resid 61...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASN(chain A and (resid 22 through 54 or resid 61...AA22 - 5448 - 80
12LEULEULEULEU(chain A and (resid 22 through 54 or resid 61...AA61 - 15787 - 183
13LEULEUALAALA(chain A and (resid 22 through 54 or resid 61...AA159 - 175185 - 201
14THRTHRPHEPHE(chain A and (resid 22 through 54 or resid 61...AA183 - 403209 - 429
15ASPASPLEULEU(chain A and (resid 22 through 54 or resid 61...AA438 - 473464 - 499
21VALVALASNASN(chain B and (resid 22 through 54 or resid 61...BB22 - 5448 - 80
22LEULEULEULEU(chain B and (resid 22 through 54 or resid 61...BB61 - 15787 - 183
23LEULEUPHEPHE(chain B and (resid 22 through 54 or resid 61...BB159 - 403185 - 429
24ASPASPLEULEU(chain B and (resid 22 through 54 or resid 61...BB438 - 473464 - 499
31VALVALASNASN(chain C and (resid 22 through 54 or resid 61...CC22 - 5448 - 80
32LEULEULEULEU(chain C and (resid 22 through 54 or resid 61...CC61 - 15787 - 183
33LEULEUALAALA(chain C and (resid 22 through 54 or resid 61...CC159 - 175185 - 201
34THRTHRPHEPHE(chain C and (resid 22 through 54 or resid 61...CC183 - 403209 - 429
35ASPASPLEULEU(chain C and (resid 22 through 54 or resid 61...CC438 - 473464 - 499
41VALVALASNASN(chain D and (resid 22 through 54 or resid 61...DD22 - 5448 - 80
42LEULEULEULEU(chain D and (resid 22 through 54 or resid 61...DD61 - 15787 - 183
43LEULEUALAALA(chain D and (resid 22 through 54 or resid 61...DD159 - 175185 - 201
44THRTHRLEULEU(chain D and (resid 22 through 54 or resid 61...DD183 - 473209 - 499
51VALVALLEULEU(chain E and (resid 22 through 157 or resid 159 through 175 or resid 183 through 473))EE22 - 15748 - 183
52LEULEUALAALA(chain E and (resid 22 through 157 or resid 159 through 175 or resid 183 through 473))EE159 - 175185 - 201
53THRTHRLEULEU(chain E and (resid 22 through 157 or resid 159 through 175 or resid 183 through 473))EE183 - 473209 - 499
61VALVALASNASN(chain F and (resid 22 through 54 or resid 61...FF22 - 5448 - 80
62LEULEULEULEU(chain F and (resid 22 through 54 or resid 61...FF61 - 15787 - 183
63LEULEUALAALA(chain F and (resid 22 through 54 or resid 61...FF159 - 175185 - 201
64THRTHRPHEPHE(chain F and (resid 22 through 54 or resid 61...FF183 - 403209 - 429
65ASPASPLEULEU(chain F and (resid 22 through 54 or resid 61...FF438 - 473464 - 499
71VALVALASNASN(chain G and (resid 22 through 54 or resid 61...GG22 - 5448 - 80
72LEULEULEULEU(chain G and (resid 22 through 54 or resid 61...GG61 - 15787 - 183
73LEULEUPHEPHE(chain G and (resid 22 through 54 or resid 61...GG159 - 403185 - 429
74ASPASPLEULEU(chain G and (resid 22 through 54 or resid 61...GG438 - 473464 - 499
81VALVALASNASN(chain H and (resid 22 through 54 or resid 61...HH22 - 5448 - 80
82LEULEULEULEU(chain H and (resid 22 through 54 or resid 61...HH61 - 15787 - 183
83LEULEUALAALA(chain H and (resid 22 through 54 or resid 61...HH159 - 175185 - 201
84THRTHRPHEPHE(chain H and (resid 22 through 54 or resid 61...HH183 - 403209 - 429
85ASPASPLEULEU(chain H and (resid 22 through 54 or resid 61...HH438 - 473464 - 499
91VALVALASNASN(chain I and (resid 22 through 54 or resid 61...II22 - 5448 - 80
92LEULEULEULEU(chain I and (resid 22 through 54 or resid 61...II61 - 15787 - 183
93LEULEUALAALA(chain I and (resid 22 through 54 or resid 61...II159 - 175185 - 201
94THRTHRLEULEU(chain I and (resid 22 through 54 or resid 61...II183 - 473209 - 499
101VALVALASNASN(chain J and (resid 22 through 54 or resid 61...JJ22 - 5448 - 80
102LEULEULEULEU(chain J and (resid 22 through 54 or resid 61...JJ61 - 15787 - 183
103LEULEUALAALA(chain J and (resid 22 through 54 or resid 61...JJ159 - 175185 - 201
104THRTHRLEULEU(chain J and (resid 22 through 54 or resid 61...JJ183 - 473209 - 499
111VALVALASNASN(chain K and (resid 22 through 54 or resid 61...KK22 - 5448 - 80
112LEULEULEULEU(chain K and (resid 22 through 54 or resid 61...KK61 - 15787 - 183
113LEULEUALAALA(chain K and (resid 22 through 54 or resid 61...KK159 - 175185 - 201
114VALVALLEULEU(chain K and (resid 22 through 54 or resid 61...KK21 - 47347 - 499
121VALVALASNASN(chain L and (resid 22 through 54 or resid 61...LL22 - 5448 - 80
122LEULEULEULEU(chain L and (resid 22 through 54 or resid 61...LL61 - 15787 - 183
123LEULEUPHEPHE(chain L and (resid 22 through 54 or resid 61...LL159 - 403185 - 429
124ASPASPLEULEU(chain L and (resid 22 through 54 or resid 61...LL438 - 473464 - 499
131VALVALASNASN(chain M and (resid 22 through 54 or resid 61...MM22 - 5448 - 80
132LEULEULEULEU(chain M and (resid 22 through 54 or resid 61...MM61 - 15787 - 183
133LEULEUALAALA(chain M and (resid 22 through 54 or resid 61...MM159 - 175185 - 201
134LYSLYSLEULEU(chain M and (resid 22 through 54 or resid 61...MM20 - 47346 - 499
141VALVALASNASN(chain N and (resid 22 through 54 or resid 61...NN22 - 5448 - 80
142LEULEULEULEU(chain N and (resid 22 through 54 or resid 61...NN61 - 15787 - 183
143LEULEUALAALA(chain N and (resid 22 through 54 or resid 61...NN159 - 175185 - 201
144THRTHRLEULEU(chain N and (resid 22 through 54 or resid 61...NN183 - 473209 - 499
151VALVALASNASN(chain O and (resid 22 through 54 or resid 61...OO22 - 5448 - 80
152LEULEULEULEU(chain O and (resid 22 through 54 or resid 61...OO61 - 15787 - 183
153LEULEUALAALA(chain O and (resid 22 through 54 or resid 61...OO159 - 175185 - 201
154THRTHRLEULEU(chain O and (resid 22 through 54 or resid 61...OO183 - 473209 - 499
161VALVALASNASN(chain P and (resid 22 through 54 or resid 61...PP22 - 5448 - 80
162LEULEULEULEU(chain P and (resid 22 through 54 or resid 61...PP61 - 15787 - 183
163LEULEUALAALA(chain P and (resid 22 through 54 or resid 61...PP159 - 175185 - 201
164THRTHRPHEPHE(chain P and (resid 22 through 54 or resid 61...PP183 - 403209 - 429
165ASPASPLEULEU(chain P and (resid 22 through 54 or resid 61...PP438 - 473464 - 499
171VALVALASNASN(chain Q and (resid 22 through 54 or resid 61...QQ22 - 5448 - 80
172LEULEULEULEU(chain Q and (resid 22 through 54 or resid 61...QQ61 - 15787 - 183
173LEULEUPHEPHE(chain Q and (resid 22 through 54 or resid 61...QQ159 - 403185 - 429
174ASPASPLEULEU(chain Q and (resid 22 through 54 or resid 61...QQ438 - 473464 - 499
181VALVALASNASN(chain R and (resid 22 through 54 or resid 61...RR22 - 5448 - 80
182LEULEULEULEU(chain R and (resid 22 through 54 or resid 61...RR61 - 15787 - 183
183LEULEUALAALA(chain R and (resid 22 through 54 or resid 61...RR159 - 175185 - 201
184LYSLYSLEULEU(chain R and (resid 22 through 54 or resid 61...RR20 - 47346 - 499
191VALVALASNASN(chain S and (resid 22 through 54 or resid 61...SS22 - 5448 - 80
192LEULEULEULEU(chain S and (resid 22 through 54 or resid 61...SS61 - 15787 - 183
193LEULEUALAALA(chain S and (resid 22 through 54 or resid 61...SS159 - 175185 - 201
194THRTHRLEULEU(chain S and (resid 22 through 54 or resid 61...SS183 - 473209 - 499
201VALVALASNASN(chain T and (resid 22 through 54 or resid 61...TT22 - 5448 - 80
202LEULEULEULEU(chain T and (resid 22 through 54 or resid 61...TT61 - 15787 - 183
203LEULEUALAALA(chain T and (resid 22 through 54 or resid 61...TT159 - 175185 - 201
204THRTHRLEULEU(chain T and (resid 22 through 54 or resid 61...TT183 - 473209 - 499
211VALVALASNASN(chain U and (resid 22 through 54 or resid 61...UU22 - 5448 - 80
212LEULEULEULEU(chain U and (resid 22 through 54 or resid 61...UU61 - 15787 - 183
213LEULEUALAALA(chain U and (resid 22 through 54 or resid 61...UU159 - 175185 - 201
214THRTHRPHEPHE(chain U and (resid 22 through 54 or resid 61...UU183 - 403209 - 429
215ASPASPLEULEU(chain U and (resid 22 through 54 or resid 61...UU438 - 473464 - 499
221VALVALASNASN(chain V and (resid 22 through 54 or resid 61...VV22 - 5448 - 80
222LEULEULEULEU(chain V and (resid 22 through 54 or resid 61...VV61 - 15787 - 183
223LEULEUPHEPHE(chain V and (resid 22 through 54 or resid 61...VV159 - 403185 - 429
224ASPASPLEULEU(chain V and (resid 22 through 54 or resid 61...VV438 - 473464 - 499
231VALVALASNASN(chain W and (resid 22 through 54 or resid 61...WW22 - 5448 - 80
232LEULEULEULEU(chain W and (resid 22 through 54 or resid 61...WW61 - 15787 - 183
233LEULEUALAALA(chain W and (resid 22 through 54 or resid 61...WW159 - 175185 - 201
234THRTHRPHEPHE(chain W and (resid 22 through 54 or resid 61...WW183 - 403209 - 429
235ASPASPLEULEU(chain W and (resid 22 through 54 or resid 61...WW438 - 473464 - 499
241VALVALASNASN(chain X and (resid 22 through 54 or resid 61...XX22 - 5448 - 80
242LEULEULEULEU(chain X and (resid 22 through 54 or resid 61...XX61 - 15787 - 183
243LEULEUALAALA(chain X and (resid 22 through 54 or resid 61...XX159 - 175185 - 201
244THRTHRLEULEU(chain X and (resid 22 through 54 or resid 61...XX183 - 473209 - 499
251VALVALASNASN(chain Y and (resid 22 through 54 or resid 61...YY22 - 5448 - 80
252LEULEULEULEU(chain Y and (resid 22 through 54 or resid 61...YY61 - 15787 - 183
253LEULEUALAALA(chain Y and (resid 22 through 54 or resid 61...YY159 - 175185 - 201
254THRTHRLEULEU(chain Y and (resid 22 through 54 or resid 61...YY183 - 473209 - 499
261VALVALASNASN(chain Z and (resid 22 through 54 or resid 61...ZZ22 - 5448 - 80
262LEULEULEULEU(chain Z and (resid 22 through 54 or resid 61...ZZ61 - 15787 - 183
263LEULEUALAALA(chain Z and (resid 22 through 54 or resid 61...ZZ159 - 175185 - 201
264VALVALLEULEU(chain Z and (resid 22 through 54 or resid 61...ZZ21 - 47347 - 499
271VALVALASNASN(chain a and (resid 22 through 54 or resid 61...aAA22 - 5448 - 80
272LEULEULEULEU(chain a and (resid 22 through 54 or resid 61...aAA61 - 15787 - 183
273LEULEUPHEPHE(chain a and (resid 22 through 54 or resid 61...aAA159 - 403185 - 429
274ASPASPLEULEU(chain a and (resid 22 through 54 or resid 61...aAA438 - 473464 - 499
281VALVALASNASN(chain b and (resid 22 through 54 or resid 61...bBA22 - 5448 - 80
282LEULEULEULEU(chain b and (resid 22 through 54 or resid 61...bBA61 - 15787 - 183
283LEULEUALAALA(chain b and (resid 22 through 54 or resid 61...bBA159 - 175185 - 201
284THRTHRPHEPHE(chain b and (resid 22 through 54 or resid 61...bBA183 - 403209 - 429
285ASPASPLEULEU(chain b and (resid 22 through 54 or resid 61...bBA438 - 473464 - 499
291VALVALASNASN(chain c and (resid 22 through 54 or resid 61...cCA22 - 5448 - 80
292LEULEULEULEU(chain c and (resid 22 through 54 or resid 61...cCA61 - 15787 - 183
293LEULEUALAALA(chain c and (resid 22 through 54 or resid 61...cCA159 - 175185 - 201
294THRTHRLEULEU(chain c and (resid 22 through 54 or resid 61...cCA183 - 473209 - 499
301VALVALASNASN(chain d and (resid 22 through 54 or resid 61...dDA22 - 5448 - 80
302LEULEULEULEU(chain d and (resid 22 through 54 or resid 61...dDA61 - 15787 - 183
303LEULEUALAALA(chain d and (resid 22 through 54 or resid 61...dDA159 - 175185 - 201
304THRTHRLEULEU(chain d and (resid 22 through 54 or resid 61...dDA183 - 473209 - 499
311VALVALASNASN(chain e and (resid 22 through 54 or resid 61...eEA22 - 5448 - 80
312LEULEULEULEU(chain e and (resid 22 through 54 or resid 61...eEA61 - 15787 - 183
313LEULEUALAALA(chain e and (resid 22 through 54 or resid 61...eEA159 - 175185 - 201
314LYSLYSLEULEU(chain e and (resid 22 through 54 or resid 61...eEA20 - 47346 - 499
321VALVALASNASN(chain f and (resid 22 through 54 or resid 61...fFA22 - 5448 - 80
322LEULEULEULEU(chain f and (resid 22 through 54 or resid 61...fFA61 - 15787 - 183
323LEULEUPHEPHE(chain f and (resid 22 through 54 or resid 61...fFA159 - 403185 - 429
324ASPASPLEULEU(chain f and (resid 22 through 54 or resid 61...fFA438 - 473464 - 499
331VALVALASNASN(chain g and (resid 22 through 54 or resid 61...gGA22 - 5448 - 80
332LEULEULEULEU(chain g and (resid 22 through 54 or resid 61...gGA61 - 15787 - 183
333LEULEUALAALA(chain g and (resid 22 through 54 or resid 61...gGA159 - 175185 - 201
334THRTHRPHEPHE(chain g and (resid 22 through 54 or resid 61...gGA183 - 403209 - 429
335ASPASPLEULEU(chain g and (resid 22 through 54 or resid 61...gGA438 - 473464 - 499
341VALVALASNASN(chain h and (resid 22 through 54 or resid 61...hHA22 - 5448 - 80
342LEULEULEULEU(chain h and (resid 22 through 54 or resid 61...hHA61 - 15787 - 183
343LEULEUALAALA(chain h and (resid 22 through 54 or resid 61...hHA159 - 175185 - 201
344THRTHRLEULEU(chain h and (resid 22 through 54 or resid 61...hHA183 - 473209 - 499
351VALVALASNASN(chain i and (resid 22 through 54 or resid 61...iIA22 - 5448 - 80
352LEULEULEULEU(chain i and (resid 22 through 54 or resid 61...iIA61 - 15787 - 183
353LEULEUALAALA(chain i and (resid 22 through 54 or resid 61...iIA159 - 175185 - 201
354THRTHRLEULEU(chain i and (resid 22 through 54 or resid 61...iIA183 - 473209 - 499
361VALVALASNASN(chain j and (resid 22 through 54 or resid 61...jJA22 - 5448 - 80
362LEULEULEULEU(chain j and (resid 22 through 54 or resid 61...jJA61 - 15787 - 183
363LEULEUALAALA(chain j and (resid 22 through 54 or resid 61...jJA159 - 175185 - 201
364THRTHRPHEPHE(chain j and (resid 22 through 54 or resid 61...jJA183 - 403209 - 429
365ASPASPLEULEU(chain j and (resid 22 through 54 or resid 61...jJA438 - 473464 - 499
371VALVALASNASN(chain k and (resid 22 through 54 or resid 61...kKA22 - 5448 - 80
372LEULEULEULEU(chain k and (resid 22 through 54 or resid 61...kKA61 - 15787 - 183
373LEULEUPHEPHE(chain k and (resid 22 through 54 or resid 61...kKA159 - 403185 - 429
374ASPASPLEULEU(chain k and (resid 22 through 54 or resid 61...kKA438 - 473464 - 499
381VALVALASNASN(chain l and (resid 22 through 54 or resid 61...lLA22 - 5448 - 80
382LEULEULEULEU(chain l and (resid 22 through 54 or resid 61...lLA61 - 15787 - 183
383LEULEUALAALA(chain l and (resid 22 through 54 or resid 61...lLA159 - 175185 - 201
384THRTHRPHEPHE(chain l and (resid 22 through 54 or resid 61...lLA183 - 403209 - 429
385ASPASPLEULEU(chain l and (resid 22 through 54 or resid 61...lLA438 - 473464 - 499
391VALVALASNASN(chain m and (resid 22 through 54 or resid 61...mMA22 - 5448 - 80
392LEULEULEULEU(chain m and (resid 22 through 54 or resid 61...mMA61 - 15787 - 183
393LEULEUALAALA(chain m and (resid 22 through 54 or resid 61...mMA159 - 175185 - 201
394THRTHRLEULEU(chain m and (resid 22 through 54 or resid 61...mMA183 - 473209 - 499
401VALVALASNASN(chain n and (resid 22 through 54 or resid 61...nNA22 - 5448 - 80
402LEULEULEULEU(chain n and (resid 22 through 54 or resid 61...nNA61 - 15787 - 183
403LEULEUALAALA(chain n and (resid 22 through 54 or resid 61...nNA159 - 175185 - 201
404THRTHRLEULEU(chain n and (resid 22 through 54 or resid 61...nNA183 - 473209 - 499

-
要素

#1: タンパク質 ...
Major capsid protein L1


分子量: 59144.301 Da / 分子数: 40 / 変異: S80N, N82T, N84A, V87L, C202S, T375K, G378S, D383E / 由来タイプ: 組換発現
由来: (組換発現) Human papillomavirus type 58 (パピローマウイルス)
遺伝子: L1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): ER2566 / 参照: UniProt: P26535

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.23 Å3/Da / 溶媒含有率: 44.89 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.2M calcium acetate, 18% (w/v) PEG 3350

-
データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U1 / 波長: 0.9795 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年7月8日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9795 Å / 相対比: 1
反射解像度: 3.5→50 Å / Num. obs: 248099 / % possible obs: 97 % / 冗長度: 1.9 % / Biso Wilson estimate: 63.48 Å2 / Rsym value: 0.171 / Net I/σ(I): 4.8
反射 シェル解像度: 3.5→3.56 Å / Num. unique obs: 11253 / Rsym value: 0.645

-
解析

ソフトウェア
名称バージョン分類
HKL-2000データスケーリング
PHENIX1.11.1_2575精密化
PDB_EXTRACT3.24データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5Y9E

5y9e


解像度: 3.5→41.551 Å / SU ML: 0.48 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 41.74
Rfactor反射数%反射
Rfree0.3402 12024 4.85 %
Rwork0.315 --
obs0.3162 248099 95.92 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 470.31 Å2 / Biso mean: 105.5379 Å2 / Biso min: 21.32 Å2
精密化ステップサイクル: final / 解像度: 3.5→41.551 Å
タンパク質核酸リガンド溶媒全体
原子数133051 0 0 0 133051
残基数----16652
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003136654
X-RAY DIFFRACTIONf_angle_d0.616185386
X-RAY DIFFRACTIONf_chiral_restr0.04419769
X-RAY DIFFRACTIONf_plane_restr0.00424197
X-RAY DIFFRACTIONf_dihedral_angle_d12.79281132
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A79615X-RAY DIFFRACTION9.516TORSIONAL
12B79615X-RAY DIFFRACTION9.516TORSIONAL
13C79615X-RAY DIFFRACTION9.516TORSIONAL
14D79615X-RAY DIFFRACTION9.516TORSIONAL
15E79615X-RAY DIFFRACTION9.516TORSIONAL
16F79615X-RAY DIFFRACTION9.516TORSIONAL
17G79615X-RAY DIFFRACTION9.516TORSIONAL
18H79615X-RAY DIFFRACTION9.516TORSIONAL
19I79615X-RAY DIFFRACTION9.516TORSIONAL
110J79615X-RAY DIFFRACTION9.516TORSIONAL
111K79615X-RAY DIFFRACTION9.516TORSIONAL
112L79615X-RAY DIFFRACTION9.516TORSIONAL
113M79615X-RAY DIFFRACTION9.516TORSIONAL
114N79615X-RAY DIFFRACTION9.516TORSIONAL
115O79615X-RAY DIFFRACTION9.516TORSIONAL
116P79615X-RAY DIFFRACTION9.516TORSIONAL
117Q79615X-RAY DIFFRACTION9.516TORSIONAL
118R79615X-RAY DIFFRACTION9.516TORSIONAL
119S79615X-RAY DIFFRACTION9.516TORSIONAL
120T79615X-RAY DIFFRACTION9.516TORSIONAL
121U79615X-RAY DIFFRACTION9.516TORSIONAL
122V79615X-RAY DIFFRACTION9.516TORSIONAL
123W79615X-RAY DIFFRACTION9.516TORSIONAL
124X79615X-RAY DIFFRACTION9.516TORSIONAL
125Y79615X-RAY DIFFRACTION9.516TORSIONAL
126Z79615X-RAY DIFFRACTION9.516TORSIONAL
127a79615X-RAY DIFFRACTION9.516TORSIONAL
128b79615X-RAY DIFFRACTION9.516TORSIONAL
129c79615X-RAY DIFFRACTION9.516TORSIONAL
130d79615X-RAY DIFFRACTION9.516TORSIONAL
131e79615X-RAY DIFFRACTION9.516TORSIONAL
132f79615X-RAY DIFFRACTION9.516TORSIONAL
133g79615X-RAY DIFFRACTION9.516TORSIONAL
134h79615X-RAY DIFFRACTION9.516TORSIONAL
135i79615X-RAY DIFFRACTION9.516TORSIONAL
136j79615X-RAY DIFFRACTION9.516TORSIONAL
137k79615X-RAY DIFFRACTION9.516TORSIONAL
138l79615X-RAY DIFFRACTION9.516TORSIONAL
139m79615X-RAY DIFFRACTION9.516TORSIONAL
140n79615X-RAY DIFFRACTION9.516TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4948-3.53440.37423450.37166374671978
3.5344-3.5760.39293920.37237969836197
3.576-3.61960.38073440.36068056840097
3.6196-3.66540.37984310.3617965839697
3.6654-3.71360.38753700.35517991836197
3.7136-3.76440.36174560.34357918837497
3.7644-3.81820.36844110.34538023843498
3.8182-3.87510.38094030.34627995839898
3.8751-3.93560.36644670.33197945841298
3.9356-4.00010.3474730.33757998847198
4.0001-4.0690.34924380.33167868830698
4.069-4.14290.3643920.3338080847298
4.1429-4.22260.33264120.31847895830797
4.2226-4.30870.3434510.31328052850397
4.3087-4.40220.32284530.31758009846298
4.4022-4.50450.33413940.30657931832597
4.5045-4.6170.36284000.31258021842197
4.617-4.74170.32023740.2948019839397
4.7417-4.8810.30684320.28647935836797
4.881-5.03830.32323590.29278028838797
5.0383-5.21810.32323440.30088023836797
5.2181-5.42650.34363620.28868000836297
5.4265-5.67290.3254580.30147856831497
5.6729-5.97120.33713880.2997948833696
5.9712-6.34410.32744310.30637749818096
6.3441-6.8320.33073100.30867890820095
6.832-7.51580.30523900.30528186857699
7.5158-8.5950.31544260.29278129855599
8.595-10.79730.31874270.2897761818895
10.7973-41.55430.32432910.28576461675278
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2520.0624-0.07090.33870.24650.40790.1640.214-0.1705-0.21930.1467-0.04520.01790.07090.36520.30950.1732-0.1312-0.0241-0.16850.303116.3632-157.4591-51.3185
20.10820.0111-0.08860.1512-0.10480.2945-0.0221-0.0786-0.2210.00910.0565-0.1196-0.06380.09930.06380.3535-0.1932-0.077-0.0984-0.01790.312912.1194-149.0859-19.1055
30.00380.0087-0.00480.0410.02510.024-0.1206-0.2845-0.29330.29760.0739-0.10390.33880.02220.00040.48810.0245-0.04970.24560.00820.461918.1744-164.0408-20.5884
40.0499-0.02920.00170.30170.05460.09970.18640.1091-0.160.01490.0196-0.21570.0125-0.01660.25020.5029-0.0047-0.19220.18370.1180.279619.3601-154.736-21.5534
50.24430.060.01910.0250.04570.0927-0.11780.2685-0.0508-0.05780.01510.0219-0.0777-0.00330.01130.4511-0.0823-0.04260.43520.19010.237420.9366-145.2436-24.2149
60.12250.19170.10580.38220.00840.23480.12530.1326-0.1905-0.05230.1754-0.1105-0.03780.13740.3630.23580.1043-0.0716-0.2045-0.18640.203914.7662-154.2712-47.6568
70.0350.0234-0.0370.025-0.02960.0238-0.09080.07270.066-0.0246-0.0289-0.01160.0040.0583-0.19030.44140.0370.05550.4760.39610.3717.0386-118.0192-60.7472
80.0235-0.04770.02860.1646-0.07060.02730.0258-0.01440.1334-0.09970.05680.1126-0.1078-0.13540.04150.10650.0766-0.09430.27890.25420.35430.9322-114.429-49.6544
90.1655-0.0498-0.00340.1976-0.0021-0.0033-0.03530.29840.0907-0.10830.10610.1276-0.0258-0.01750.12430.45970.0748-0.22680.13530.18710.34396.4076-125.3196-39.4618
10-0.00290.0034-0.0070.02950.01960.01660.00460.06120.0226-0.08510.0211-0.0452-0.04170.06120.08670.29230.05920.00580.05810.17570.372.9171-134.3889-38.9806
110.07160.0234-0.03610.119-0.02890.10030.00450.01070.03420.036-0.05870.00720.0715-0.0108-0.11020.37420.014-0.08480.19810.20990.271711.8644-132.4728-32.9956
120.1169-0.0680.06640.2318-0.00850.0479-0.01380.09140.2795-0.2351-0.05830.2135-0.0332-0.10070.08050.03310.322-0.16410.33820.50710.26069.954-116.0364-52.8048
130.05830.0365-0.00610.0407-0.00920.07690.1466-0.0375-0.2198-0.0994-0.1487-0.1440.1968-0.0796-0.01760.39660.0285-0.2190.09550.18230.525644.7457-161.3814-19.0206
140.29850.0417-0.07540.279-0.01490.13470.3345-0.5113-0.53680.3934-0.2485-0.26070.1490.20480.28420.15460.1038-0.2459-0.3970.4592-0.011639.3869-149.0774-12.9551
150.0020.00050.0060.03580.01570.02210.0392-0.03070.12750.07020.0774-0.18510.0242-0.10190.12420.3527-0.2751-0.05230.13190.14560.307157.6262-122.7438-8.2464
160.09910.04080.22230.38960.01420.508-0.00120.0096-0.04120.1244-0.11380.033-0.0063-0.3264-0.49630.28260.00940.0190.32270.20140.163138.6432-121.1174-8.6025
170.0322-0.0842-0.00070.2699-0.13250.5064-0.0029-0.08030.23690.1299-0.03440.1841-0.2291-0.13650.04530.3545-0.1974-0.01550.2813-0.18080.596340.0395-101.9746-6.582
180.64220.25160.10630.6080.04190.3160.1637-0.39160.46490.1661-0.40450.02120.1409-0.2333-0.62040.2805-0.21970.0069-0.36330.19920.260244.9573-119.8504-10.4987
190.0804-0.0764-0.01740.10060.03470.0292-0.0886-0.07870.2146-0.1903-0.0817-0.26840.12380.0186-0.27430.4262-0.04420.013-0.02140.25080.736535.8271-96.105-31.405
200.14210.0651-0.0650.30030.06940.04530.1107-0.03490.79710.2907-0.32030.32190.2644-0.4972-0.72550.00120.3864-0.0934-0.44290.45510.546623.1708-104.6205-28.7075
210.20190.05420.0352-0.00160.02280.01490.05170.13170.0178-0.0206-0.05950.07750.0060.04540.03670.245-0.16030.35930.5435-0.35420.5965-53.1768-51.657525.9778
220.00850.0070.0217-0.0152-0.00420.01450.0138-0.02230.1318-0.032-0.0407-0.1666-0.03730.08-0.0120.5639-0.21540.49781.335-0.09290.8696-32.2459-31.69519.0467
230.33140.15240.09290.0556-0.00630.1222-0.26730.41550.0341-0.0318-0.14590.1137-0.09130.2995-0.16560.1907-0.18790.55311.1536-0.05590.6304-42.8511-30.10029.1228
240.02670.04080.0221-0.00880.00560.0224-0.08880.22690.129-0.017-0.07120.0339-0.05520.1709-0.13760.41510.0120.45020.7226-0.22740.6613-35.9071-28.271518.7021
250.0134-0.05370.04430.0785-0.0420.06520.07860.3197-0.0111-0.0221-0.0746-0.00130.20990.2314-00.527-0.01540.34360.6417-0.62260.6771-48.1872-50.133725.0749
260.03420.02550.01390.041-0.0310.0320.13920.06440.0147-0.0032-0.2574-0.07840.11730.1778-01.03580.00370.11181.2175-0.23730.7615-19.4923-51.892650.5352
270.0470.02150.01460.01790.01550.0180.0969-0.04140.19440.1291-0.0629-0.02610.13630.020500.9999-0.3060.21311.4006-0.43391.042-20.5225-55.076355.7691
280.02640.0245-0.01180.0202-0.01250.00660.0210.0020.05020.0401-0.05220.0080.08380.0171-01.1612-0.15340.26371.67-0.20011.2583-11.4052-38.780913.6443
290.02830.00080.00160.01750.00310.01580.1609-0.02140.09030.0929-0.035-0.0982-0.06110.104701.0370.04850.37541.3125-0.32881.037-22.6086-50.440729.3364
300.00110.0014-0.00190.0001-00.00340.0075-0.01110.046-0.00690.0145-0.0180.00970.022800.9367-0.0130.25551.3471-0.07380.8448-21.8513-53.35630.2765
310.03120.0060.018-0.0056-0.0010.0290.0661-0.07080.17770.0622-0.33510.07540.03060.0193-0.00010.9326-0.10040.19511.2711-0.280.769-23.8192-47.938324.5986
320.01720.008-0.00580.0082-0.03160.0230.22890.04080.2360.2124-0.20490.0233-0.10630.10400.8429-0.19060.20891.3579-0.43180.9633-24.5145-42.88135.3787
330.04990.05160.02860.06360.05920.09080.03660.19240.0329-0.0961-0.32330.02570.09940.0833-0.00070.919-0.36460.34111.3213-0.01651.0071-4.0584-41.397541.5163
34-0.00060-0.00220.0137-0.00690.0015-0.0520.0067-0.01460.0265-0.0587-0.04670.05610.1077-01.07920.06050.0320.9578-0.31450.9077-27.3952-65.842453.3046
350.00930.0084-0.00120.00750.00190.00310.0597-0.0022-0.00150.05860.0477-0.0148-0.08740.009901.1262-0.19780.09911.3664-0.27180.9762-23.1086-42.463364.8974
360.0055-0.012-0.0219-0.02070.0040.0044-0.07350.0967-0.0039-0.07360.0622-0.0437-0.10460.0298-00.7249-0.12210.46551.28420.11280.947-55.5857-10.897815.0972
370.0033-0.004-0.0041-0.00350.0015-0.0053-0.0103-0.05030.0220.0619-0.01020.2219-0.0684-0.08600.8279-0.22550.55031.10270.21811.041-69.0903-9.605124.9789
380.08860.06390.04530.0180.03990.0159-0.0560.07350.07950.0288-0.05920.1804-0.10850.0044-0.22980.7606-0.57960.49541.2030.36450.7997-34.7119-3.798813.8455
39-0.00570.008-0.0145-0.0141-0.01360.029-0.07780.15960.09910.1261-0.0531-0.0685-0.04690.2552-0.01720.6731-0.61760.07731.21550.05940.5879-27.9599-7.602720.5891
400.11610.02760.13060.05150.0230.12740.00720.54390.0960.1050.05950.0653-0.20490.26610.02420.5747-0.26210.32330.68640.17950.7282-57.4256-12.811417.9601
41-0.0061-0.003-0.011-0.0122-0.0037-0.0024-0.00910.10570.05170.0383-0.109-0.04570.05830.1219-01.5506-0.1063-0.17681.19870.21351.1847-32.71510.112841.4761
42-0.00140.0018-0.0042-0.00130.0054-0.0002-0.04960.00740.00160.00120.02350.0281-0.0731-0.0063-00.9863-0.32-0.00491.15230.06331.0498-30.022815.160936.9452
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1310.00020.01070.00410.01060.01040.00360.02950.00960.122-0.0037-0.0534-0.0666-0.0006-0.002701.134-0.40040.21151.2748-0.08941.412465.7683-4.2906-18.4078
132-0.0034-0.00140.00040.00270.01430.0028-0.0890.0769-0.0804-0.0464-0.0549-0.1326-0.0741-0.0362-00.8862-0.37750.31861.2156-0.30711.309363.4876-16.7656-15.6325
1330.005-0.01560.01110.00320.00890.0154-0.3739-0.17690.11710.058-0.1425-0.0682-0.0284-0.0722-0.00261.00670.31450.04031.0782-0.21461.154331.45079.5145-31.8056
1340.08720.0590.0470.0223-0.01170.1725-0.0914-0.30930.2535-0.1133-0.22570.01090.0439-0.8018-0.0041.40340.4690.03541.4306-0.12071.148119.71350.3904-28.4805
1350.03380.00360.01820.0157-0.12330.17030.02350.0059-0.0762-0.197-0.20820.1210.1792-0.1739-0.3921.2966-0.0906-0.60061.50960.77430.4606-52.303-98.8031-75.1913
1360.1594-0.08470.05640.1348-0.08870.20720.14870.10940.1066-0.3720.02150.10040.1862-0.23020.28780.74630.038-0.30171.63981.13510.6171-49.4889-86.7637-78.6083
1370.02470.04340.03490.09540.04570.0587-0.04030.0493-0.0135-0.3691-0.0099-0.02170.0079-0.05010.13751.4007-0.1234-0.29461.42380.49980.7188-53.7864-106.9607-66.9931
1380.08460.0537-0.07720.0688-0.10530.1112-0.18960.1204-0.1874-0.0771-0.2604-0.23280.2220.3804-0.48870.41240.33230.01771.0430.80570.5974-27.3757-103.7814-43.5474
1390.18160.09770.01280.2224-0.09890.2294-0.2370.1459-0.0816-0.2510.03770.060.05110.1655-0.12730.5190.2601-0.07020.64430.26430.2235-26.4984-97.1144-68.7523
140-0.00030.00610.00590.00910.00790.0062-0.11130.0355-0.1114-0.0963-0.05660.00940.0466-0.0118-0.00011.16920.08660.45031.06730.01240.6642-30.8396-108.9656-65.6291
1410.0898-0.0058-0.05240.01610.04660.1439-0.39640.1289-0.1168-0.1828-0.0959-0.13120.32130.0145-0.41880.72450.00420.11090.9790.24450.1692-31.6908-101.273-61.6979
1420.33590.1514-0.28230.1658-0.28380.5886-0.43680.1593-0.1359-0.14280.00050.03650.07980.1251-0.57770.45980.01390.00890.74760.45960.2986-33.3682-96.977-62.3555
1430.4713-0.0698-0.25810.04630.06960.4066-0.34770.0864-0.0978-0.0462-0.4462-0.44950.17310.7643-1.69140.47660.15490.02151.02060.90430.2174-25.3981-102.8861-40.7959
1440.02420.00440.01490.00290.00680.0080.01150.08-0.04360.18790.07260.04040.00680.08630.09771.37640.1662-0.21191.27610.81830.8826-65.7417-69.734-80.6223
1450.0411-0.06290.0890.1268-0.10320.1882-0.0306-0.09280.031-0.1549-0.1020.0914-0.1071-0.1944-0.18951.4370.696-0.23851.50680.96160.8839-56.2595-67.0711-77.9756
1460.1605-0.00480.17810.0917-0.09030.1232-0.1056-0.00250.303-0.1471-0.41490.2235-0.1069-0.0685-1.02811.45190.7419-0.09951.86311.46680.6527-55.9378-65.3781-77.4159
1470.1171-0.1250.05060.3048-0.1140.1481-0.1037-0.09470.40590.0361-0.11570.3183-0.19520.0061-0.61341.26480.51180.06631.19241.08731.0909-39.7408-48.0099-60.3299
1480.0390.01610.02930.0064-0.00430.03960.0895-0.00480.07080.0570.15810.02220.08370.0330.44571.69530.25020.03761.06710.86820.9915-25.2582-50.2188-56.6815
1490.0812-0.12420.12750.0773-0.13860.243-0.1153-0.08310.29540.011-0.0978-0.0502-0.2843-0.0677-0.53231.49060.45120.30521.35241.10450.9719-39.2054-51.6454-58.3589
1500.06740.05690.01180.11080.00580.0360.1777-0.09970.18070.1014-0.00490.0253-0.0642-0.10840.03141.8115-0.90660.28381.23450.01260.5587-18.3337-65.9086-28.4377
1510.16430.191-0.12540.1647-0.18150.17990.3727-0.24360.04520.4858-0.4544-0.1278-0.05320.44890.06280.8024-0.47260.11881.78930.75710.1927-14.2404-82.3358-53.6282
1520.2098-0.1168-0.07940.0980.04690.06490.1847-0.03330.38460.06810.0129-0.1873-0.23090.01210.10751.9629-1.1010.13281.48850.09440.711-18.4681-65.0715-33.7701
1530.04640.0326-0.05590.4494-0.26040.2152-0.1455-0.00940.0058-0.1447-0.20330.40570.2308-0.3054-0.55910.4621-0.36430.16111.1199-0.50220.614425.3427-104.585241.8457
1540.0421-0.02940.02390.1670.02480.1117-0.133-0.0012-0.12250.2807-0.0614-0.08440.2814-0.1696-0.17410.7456-0.42890.15481.2988-0.34810.693723.212-101.62572.8416
1550.06530.08060.05860.21510.11990.2613-0.0396-0.08210.04050.2666-0.16720.22630.0925-0.1617-0.52850.5741-0.36580.10121.4013-0.6980.422923.8634-97.354365.5845
1560.27480.15010.09220.1368-0.13030.6513-0.180.06990.0648-0.0836-0.39020.31410.1632-0.2272-0.53730.618-0.23750.12851.0563-0.320.46830.8312-107.127837.6791
1570.00980.00740.03460.0992-0.00570.2018-0.13030.14090.0694-0.15470.0451-0.0484-0.01490.2334-0.04971.0214-0.1004-0.02091.1082-0.54360.72815.415-64.201440.3709
1580.178-0.10530.08310.1354-0.02010.0384-0.0023-0.03040.0346-0.3084-0.10960.3577-0.1439-0.05870.04191.0266-0.16580.11961.1518-0.40760.754516.2435-70.188446.743
1590.05340.01750.06370.150.15690.1367-0.16350.0929-0.0725-0.1777-0.02250.1941-0.0151-0.2341-0.16220.4842-0.1483-0.0091.5677-0.64710.574114.8924-80.051852.3684
1600.14980.07960.05120.1702-0.04660.0453-0.0231-0.02620.0238-0.2528-0.08520.1024-0.0046-0.0095-00.9149-0.09040.0081.263-0.46180.985618.3721-62.144139.0819
1610.0623-0.01350.06520.04620.00310.06750.17730.1176-0.02760.2461-0.0351-0.00960.1640.12400.7869-0.18090.00081.4062-0.46970.915653.7195-108.732373.2585
1620.0867-0.0040.11230.13550.00290.11980.07270.0403-0.03520.2165-0.1951-0.0650.07020.0357-0.52860.551-0.2561-0.08421.4923-0.49520.691646.8861-91.287284.6736
1630.17120.1215-0.08510.16660.00030.21570.1444-0.0716-0.09590.1446-0.1264-0.0161-0.0288-0.17450.16750.5562-0.159-0.03641.3755-0.53560.794847.1292-90.728375.8939
1640.0905-0.0309-0.0110.3637-0.06920.0680.1150.0232-0.07780.3024-0.0079-0.17620.12450.1944-0.06930.7992-0.25880.05711.5308-0.40770.814551.4622-108.560771.0922
1650.0763-0.06040.00820.0828-0.06490.0409-0.03750.24430.02660.14250.001-0.31110.03610.1806-0.01710.7471-0.1694-0.15661.4764-0.4941.084769.5076-69.616380.5815
1660.0175-0.03370.03030.26890.01060.0421-0.03770.0566-0.02640.2081-0.04520.1335-0.01370.03730.08110.9083-0.3001-0.13680.9152-0.45190.494336.9857-61.897387.1522
1670.15190.02170.16740.09250.05160.15310.03250.0347-0.07550.0747-0.1006-0.15090.14730.1783-0.20740.5821-0.38640.00741.4716-0.56160.606747.1598-66.198682.8156
1680.10050.0179-0.02820.0352-0.01850.0627-0.06510.1304-0.10180.0768-0.1285-0.1670.03120.0766-0.0060.6943-0.1862-0.22251.5283-0.26510.914674.8796-66.651375.9151
1690.2917-0.27840.1930.2781-0.18030.126-0.00070.21530.1047-0.0823-0.1291-0.06240.08450.1665-0.17510.6836-0.5231-0.00840.8475-0.32490.64243.5767-41.958361.1457
1700.2063-0.02510.20960.2841-0.08740.4894-0.08430.3558-0.0599-0.0662-0.04140.0398-0.19410.1381-0.20390.7241-0.2678-0.01630.9358-0.38050.443231.8332-51.672362.7144
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 111 )A21 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 173 )A112 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 208 )A174 - 208
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 277 )A209 - 277
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 317 )A278 - 317
6X-RAY DIFFRACTION6chain 'A' and (resid 318 through 473 )A318 - 473
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 47 )B21 - 47
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 87 )B48 - 87
9X-RAY DIFFRACTION9chain 'B' and (resid 88 through 146 )B88 - 146
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 277 )B147 - 277
11X-RAY DIFFRACTION11chain 'B' and (resid 278 through 317 )B278 - 317
12X-RAY DIFFRACTION12chain 'B' and (resid 318 through 473 )B318 - 473
13X-RAY DIFFRACTION13chain 'C' and (resid 20 through 87 )C20 - 87
14X-RAY DIFFRACTION14chain 'C' and (resid 88 through 473 )C88 - 473
15X-RAY DIFFRACTION15chain 'D' and (resid 20 through 88 )D20 - 88
16X-RAY DIFFRACTION16chain 'D' and (resid 89 through 160 )D89 - 160
17X-RAY DIFFRACTION17chain 'D' and (resid 161 through 194 )D161 - 194
18X-RAY DIFFRACTION18chain 'D' and (resid 195 through 473 )D195 - 473
19X-RAY DIFFRACTION19chain 'E' and (resid 20 through 87 )E20 - 87
20X-RAY DIFFRACTION20chain 'E' and (resid 88 through 473 )E88 - 473
21X-RAY DIFFRACTION21chain 'F' and (resid 20 through 111 )F20 - 111
22X-RAY DIFFRACTION22chain 'F' and (resid 112 through 173 )F112 - 173
23X-RAY DIFFRACTION23chain 'F' and (resid 174 through 277 )F174 - 277
24X-RAY DIFFRACTION24chain 'F' and (resid 278 through 317 )F278 - 317
25X-RAY DIFFRACTION25chain 'F' and (resid 318 through 473 )F318 - 473
26X-RAY DIFFRACTION26chain 'G' and (resid 20 through 57 )G20 - 57
27X-RAY DIFFRACTION27chain 'G' and (resid 58 through 111 )G58 - 111
28X-RAY DIFFRACTION28chain 'G' and (resid 112 through 146 )G112 - 146
29X-RAY DIFFRACTION29chain 'G' and (resid 147 through 187 )G147 - 187
30X-RAY DIFFRACTION30chain 'G' and (resid 188 through 208 )G188 - 208
31X-RAY DIFFRACTION31chain 'G' and (resid 209 through 277 )G209 - 277
32X-RAY DIFFRACTION32chain 'G' and (resid 278 through 340 )G278 - 340
33X-RAY DIFFRACTION33chain 'G' and (resid 341 through 382 )G341 - 382
34X-RAY DIFFRACTION34chain 'G' and (resid 383 through 450 )G383 - 450
35X-RAY DIFFRACTION35chain 'G' and (resid 451 through 473 )G451 - 473
36X-RAY DIFFRACTION36chain 'H' and (resid 20 through 70 )H20 - 70
37X-RAY DIFFRACTION37chain 'H' and (resid 71 through 111 )H71 - 111
38X-RAY DIFFRACTION38chain 'H' and (resid 112 through 247 )H112 - 247
39X-RAY DIFFRACTION39chain 'H' and (resid 248 through 317 )H248 - 317
40X-RAY DIFFRACTION40chain 'H' and (resid 318 through 473 )H318 - 473
41X-RAY DIFFRACTION41chain 'I' and (resid 20 through 56 )I20 - 56
42X-RAY DIFFRACTION42chain 'I' and (resid 57 through 87 )I57 - 87
43X-RAY DIFFRACTION43chain 'I' and (resid 88 through 232 )I88 - 232
44X-RAY DIFFRACTION44chain 'I' and (resid 233 through 307 )I233 - 307
45X-RAY DIFFRACTION45chain 'I' and (resid 308 through 340 )I308 - 340
46X-RAY DIFFRACTION46chain 'I' and (resid 341 through 473 )I341 - 473
47X-RAY DIFFRACTION47chain 'J' and (resid 20 through 87 )J20 - 87
48X-RAY DIFFRACTION48chain 'J' and (resid 88 through 473 )J88 - 473
49X-RAY DIFFRACTION49chain 'K' and (resid 21 through 70 )K21 - 70
50X-RAY DIFFRACTION50chain 'K' and (resid 71 through 111 )K71 - 111
51X-RAY DIFFRACTION51chain 'K' and (resid 112 through 173 )K112 - 173
52X-RAY DIFFRACTION52chain 'K' and (resid 174 through 208 )K174 - 208
53X-RAY DIFFRACTION53chain 'K' and (resid 209 through 277 )K209 - 277
54X-RAY DIFFRACTION54chain 'K' and (resid 278 through 317 )K278 - 317
55X-RAY DIFFRACTION55chain 'K' and (resid 318 through 473 )K318 - 473
56X-RAY DIFFRACTION56chain 'L' and (resid 20 through 47 )L20 - 47
57X-RAY DIFFRACTION57chain 'L' and (resid 48 through 87 )L48 - 87
58X-RAY DIFFRACTION58chain 'L' and (resid 88 through 247 )L88 - 247
59X-RAY DIFFRACTION59chain 'L' and (resid 248 through 363 )L248 - 363
60X-RAY DIFFRACTION60chain 'L' and (resid 364 through 473 )L364 - 473
61X-RAY DIFFRACTION61chain 'M' and (resid 20 through 57 )M20 - 57
62X-RAY DIFFRACTION62chain 'M' and (resid 58 through 88 )M58 - 88
63X-RAY DIFFRACTION63chain 'M' and (resid 89 through 146 )M89 - 146
64X-RAY DIFFRACTION64chain 'M' and (resid 147 through 473 )M147 - 473
65X-RAY DIFFRACTION65chain 'N' and (resid 20 through 88 )N20 - 88
66X-RAY DIFFRACTION66chain 'N' and (resid 89 through 208 )N89 - 208
67X-RAY DIFFRACTION67chain 'N' and (resid 209 through 473 )N209 - 473
68X-RAY DIFFRACTION68chain 'O' and (resid 20 through 87 )O20 - 87
69X-RAY DIFFRACTION69chain 'O' and (resid 88 through 247 )O88 - 247
70X-RAY DIFFRACTION70chain 'O' and (resid 248 through 473 )O248 - 473
71X-RAY DIFFRACTION71chain 'P' and (resid 21 through 111 )P21 - 111
72X-RAY DIFFRACTION72chain 'P' and (resid 112 through 297 )P112 - 297
73X-RAY DIFFRACTION73chain 'P' and (resid 298 through 317 )P298 - 317
74X-RAY DIFFRACTION74chain 'P' and (resid 318 through 473 )P318 - 473
75X-RAY DIFFRACTION75chain 'Q' and (resid 20 through 111 )Q20 - 111
76X-RAY DIFFRACTION76chain 'Q' and (resid 112 through 194 )Q112 - 194
77X-RAY DIFFRACTION77chain 'Q' and (resid 195 through 363 )Q195 - 363
78X-RAY DIFFRACTION78chain 'Q' and (resid 364 through 473 )Q364 - 473
79X-RAY DIFFRACTION79chain 'R' and (resid 20 through 111 )R20 - 111
80X-RAY DIFFRACTION80chain 'R' and (resid 112 through 194 )R112 - 194
81X-RAY DIFFRACTION81chain 'R' and (resid 195 through 473 )R195 - 473
82X-RAY DIFFRACTION82chain 'S' and (resid 20 through 87 )S20 - 87
83X-RAY DIFFRACTION83chain 'S' and (resid 88 through 240 )S88 - 240
84X-RAY DIFFRACTION84chain 'S' and (resid 241 through 473 )S241 - 473
85X-RAY DIFFRACTION85chain 'T' and (resid 20 through 160 )T20 - 160
86X-RAY DIFFRACTION86chain 'T' and (resid 161 through 247 )T161 - 247
87X-RAY DIFFRACTION87chain 'T' and (resid 248 through 317 )T248 - 317
88X-RAY DIFFRACTION88chain 'T' and (resid 318 through 473 )T318 - 473
89X-RAY DIFFRACTION89chain 'U' and (resid 22 through 111 )U22 - 111
90X-RAY DIFFRACTION90chain 'U' and (resid 112 through 473 )U112 - 473
91X-RAY DIFFRACTION91chain 'V' and (resid 20 through 57 )V20 - 57
92X-RAY DIFFRACTION92chain 'V' and (resid 58 through 87 )V58 - 87
93X-RAY DIFFRACTION93chain 'V' and (resid 88 through 127 )V88 - 127
94X-RAY DIFFRACTION94chain 'V' and (resid 128 through 160 )V128 - 160
95X-RAY DIFFRACTION95chain 'V' and (resid 161 through 247 )V161 - 247
96X-RAY DIFFRACTION96chain 'V' and (resid 248 through 317 )V248 - 317
97X-RAY DIFFRACTION97chain 'V' and (resid 318 through 402 )V318 - 402
98X-RAY DIFFRACTION98chain 'V' and (resid 403 through 473 )V403 - 473
99X-RAY DIFFRACTION99chain 'W' and (resid 20 through 111 )W20 - 111
100X-RAY DIFFRACTION100chain 'W' and (resid 112 through 247 )W112 - 247
101X-RAY DIFFRACTION101chain 'W' and (resid 248 through 473 )W248 - 473
102X-RAY DIFFRACTION102chain 'X' and (resid 20 through 100 )X20 - 100
103X-RAY DIFFRACTION103chain 'X' and (resid 101 through 327 )X101 - 327
104X-RAY DIFFRACTION104chain 'X' and (resid 328 through 354 )X328 - 354
105X-RAY DIFFRACTION105chain 'X' and (resid 355 through 473 )X355 - 473
106X-RAY DIFFRACTION106chain 'Y' and (resid 20 through 87 )Y20 - 87
107X-RAY DIFFRACTION107chain 'Y' and (resid 88 through 473 )Y88 - 473
108X-RAY DIFFRACTION108chain 'Z' and (resid 21 through 111 )Z21 - 111
109X-RAY DIFFRACTION109chain 'Z' and (resid 112 through 277 )Z112 - 277
110X-RAY DIFFRACTION110chain 'Z' and (resid 278 through 340 )Z278 - 340
111X-RAY DIFFRACTION111chain 'Z' and (resid 341 through 473 )Z341 - 473
112X-RAY DIFFRACTION112chain 'a' and (resid 20 through 47 )a20 - 47
113X-RAY DIFFRACTION113chain 'a' and (resid 48 through 87 )a48 - 87
114X-RAY DIFFRACTION114chain 'a' and (resid 88 through 117 )a88 - 117
115X-RAY DIFFRACTION115chain 'a' and (resid 118 through 208 )a118 - 208
116X-RAY DIFFRACTION116chain 'a' and (resid 209 through 277 )a209 - 277
117X-RAY DIFFRACTION117chain 'a' and (resid 278 through 327 )a278 - 327
118X-RAY DIFFRACTION118chain 'a' and (resid 328 through 354 )a328 - 354
119X-RAY DIFFRACTION119chain 'a' and (resid 355 through 402 )a355 - 402
120X-RAY DIFFRACTION120chain 'a' and (resid 403 through 473 )a403 - 473
121X-RAY DIFFRACTION121chain 'b' and (resid 20 through 87 )b20 - 87
122X-RAY DIFFRACTION122chain 'b' and (resid 88 through 340 )b88 - 340
123X-RAY DIFFRACTION123chain 'b' and (resid 341 through 363 )b341 - 363
124X-RAY DIFFRACTION124chain 'b' and (resid 364 through 473 )b364 - 473
125X-RAY DIFFRACTION125chain 'c' and (resid 20 through 87 )c20 - 87
126X-RAY DIFFRACTION126chain 'c' and (resid 88 through 111 )c88 - 111
127X-RAY DIFFRACTION127chain 'c' and (resid 112 through 182 )c112 - 182
128X-RAY DIFFRACTION128chain 'c' and (resid 183 through 263 )c183 - 263
129X-RAY DIFFRACTION129chain 'c' and (resid 264 through 340 )c264 - 340
130X-RAY DIFFRACTION130chain 'c' and (resid 341 through 364 )c341 - 364
131X-RAY DIFFRACTION131chain 'c' and (resid 365 through 402 )c365 - 402
132X-RAY DIFFRACTION132chain 'c' and (resid 403 through 473 )c403 - 473
133X-RAY DIFFRACTION133chain 'd' and (resid 20 through 127 )d20 - 127
134X-RAY DIFFRACTION134chain 'd' and (resid 128 through 473 )d128 - 473
135X-RAY DIFFRACTION135chain 'e' and (resid 20 through 208 )e20 - 208
136X-RAY DIFFRACTION136chain 'e' and (resid 209 through 327 )e209 - 327
137X-RAY DIFFRACTION137chain 'e' and (resid 328 through 473 )e328 - 473
138X-RAY DIFFRACTION138chain 'f' and (resid 20 through 131 )f20 - 131
139X-RAY DIFFRACTION139chain 'f' and (resid 132 through 170 )f132 - 170
140X-RAY DIFFRACTION140chain 'f' and (resid 171 through 208 )f171 - 208
141X-RAY DIFFRACTION141chain 'f' and (resid 209 through 263 )f209 - 263
142X-RAY DIFFRACTION142chain 'f' and (resid 264 through 340 )f264 - 340
143X-RAY DIFFRACTION143chain 'f' and (resid 341 through 473 )f341 - 473
144X-RAY DIFFRACTION144chain 'g' and (resid 20 through 70 )g20 - 70
145X-RAY DIFFRACTION145chain 'g' and (resid 71 through 170 )g71 - 170
146X-RAY DIFFRACTION146chain 'g' and (resid 171 through 473 )g171 - 473
147X-RAY DIFFRACTION147chain 'h' and (resid 20 through 151 )h20 - 151
148X-RAY DIFFRACTION148chain 'h' and (resid 152 through 240 )h152 - 240
149X-RAY DIFFRACTION149chain 'h' and (resid 241 through 473 )h241 - 473
150X-RAY DIFFRACTION150chain 'i' and (resid 20 through 111 )i20 - 111
151X-RAY DIFFRACTION151chain 'i' and (resid 112 through 317 )i112 - 317
152X-RAY DIFFRACTION152chain 'i' and (resid 318 through 473 )i318 - 473
153X-RAY DIFFRACTION153chain 'j' and (resid 21 through 117 )j21 - 117
154X-RAY DIFFRACTION154chain 'j' and (resid 118 through 208 )j118 - 208
155X-RAY DIFFRACTION155chain 'j' and (resid 209 through 364 )j209 - 364
156X-RAY DIFFRACTION156chain 'j' and (resid 365 through 473 )j365 - 473
157X-RAY DIFFRACTION157chain 'k' and (resid 20 through 70 )k20 - 70
158X-RAY DIFFRACTION158chain 'k' and (resid 71 through 146 )k71 - 146
159X-RAY DIFFRACTION159chain 'k' and (resid 147 through 340 )k147 - 340
160X-RAY DIFFRACTION160chain 'k' and (resid 341 through 473 )k341 - 473
161X-RAY DIFFRACTION161chain 'l' and (resid 20 through 87 )l20 - 87
162X-RAY DIFFRACTION162chain 'l' and (resid 88 through 277 )l88 - 277
163X-RAY DIFFRACTION163chain 'l' and (resid 278 through 340 )l278 - 340
164X-RAY DIFFRACTION164chain 'l' and (resid 341 through 473 )l341 - 473
165X-RAY DIFFRACTION165chain 'm' and (resid 20 through 111 )m20 - 111
166X-RAY DIFFRACTION166chain 'm' and (resid 112 through 186 )m112 - 186
167X-RAY DIFFRACTION167chain 'm' and (resid 187 through 382 )m187 - 382
168X-RAY DIFFRACTION168chain 'm' and (resid 383 through 473 )m383 - 473
169X-RAY DIFFRACTION169chain 'n' and (resid 20 through 88 )n20 - 88
170X-RAY DIFFRACTION170chain 'n' and (resid 89 through 473 )n89 - 473

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る