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- PDB-5mub: ACC1 Fab fragment in complex with citrullinated C1 epitope of CII... -

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基本情報

登録情報
データベース: PDB / ID: 5mub
タイトルACC1 Fab fragment in complex with citrullinated C1 epitope of CII (CG05)
要素
  • (ACC1 Fab fragment heavy chain) x 2
  • ACC1 Fab fragment light chain
  • triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
キーワードIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) / Fab fragment / collagen type II / citrullinated triple-helical C1 epitope
機能・相同性
機能・相同性情報


Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / Collagen degradation ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / Collagen degradation / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / proteoglycan metabolic process / platelet-derived growth factor binding / Integrin cell surface interactions / notochord development / limb bud formation / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / limb morphogenesis / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / endochondral ossification / collagen trimer / collagen fibril organization / cartilage development / skeletal system morphogenesis / proteoglycan binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cartilage condensation / inner ear morphogenesis / roof of mouth development / inner ear development / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / ossification / extracellular matrix / skeletal system development / central nervous system development / sensory perception of sound / bone development / regulation of gene expression / collagen-containing extracellular matrix / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / cytoplasm
類似検索 - 分子機能
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Collagen alpha-1(II) chain
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Dobritzsch, D. / Holmdahl, R. / Ge, C.
資金援助 スウェーデン, 5件
組織認可番号国
Swedish Foundation for Strategic ResearchRBa08-0047 スウェーデン
Swedish Foundation for Strategic ResearchRB13-015 スウェーデン
Knut and Alice Wallenberg FoundationKAW 2010.0148 スウェーデン
Swedish Research CouncilK2011-52X-07931-25-5, 2015-02662, K2009-75SX-21029-01-3, K2012-75SX-22072-01-3 スウェーデン
European UnionIMI 115142
引用ジャーナル: JCI Insight / 年: 2017
タイトル: Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.
著者: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / ...著者: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / Burkhardt, H. / Dobritzsch, D. / Holmdahl, R.
履歴
登録2017年1月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年7月19日Provider: repository / タイプ: Initial release
改定 1.12017年9月13日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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
改定 2.12024年1月17日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: ACC1 Fab fragment heavy chain
B: ACC1 Fab fragment light chain
X: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
C: ACC1 Fab fragment heavy chain
D: ACC1 Fab fragment light chain
E: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
F: ACC1 Fab fragment heavy chain
G: ACC1 Fab fragment light chain
H: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
I: ACC1 Fab fragment heavy chain
J: ACC1 Fab fragment light chain
K: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
L: ACC1 Fab fragment heavy chain
M: ACC1 Fab fragment light chain
N: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
O: ACC1 Fab fragment heavy chain
P: ACC1 Fab fragment light chain
Q: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
R: ACC1 Fab fragment heavy chain
S: ACC1 Fab fragment light chain
T: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
U: ACC1 Fab fragment heavy chain
V: ACC1 Fab fragment light chain
W: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)401,15324
ポリマ－401,15324
非ポリマー00
水00
1
A: ACC1 Fab fragment heavy chain
B: ACC1 Fab fragment light chain
X: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,0913
ポリマ－50,0913
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-27 kcal/mol
Surface area19590 Å2
手法PISA
2
C: ACC1 Fab fragment heavy chain
D: ACC1 Fab fragment light chain
E: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,0913
ポリマ－50,0913
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-25 kcal/mol
Surface area19480 Å2
手法PISA
3
F: ACC1 Fab fragment heavy chain
G: ACC1 Fab fragment light chain
H: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,3053
ポリマ－50,3053
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-26 kcal/mol
Surface area19570 Å2
手法PISA
4
I: ACC1 Fab fragment heavy chain
J: ACC1 Fab fragment light chain
K: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,0913
ポリマ－50,0913
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-26 kcal/mol
Surface area19370 Å2
手法PISA
5
L: ACC1 Fab fragment heavy chain
M: ACC1 Fab fragment light chain
N: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,0913
ポリマ－50,0913
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-27 kcal/mol
Surface area19500 Å2
手法PISA
6
O: ACC1 Fab fragment heavy chain
P: ACC1 Fab fragment light chain
Q: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,0913
ポリマ－50,0913
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-26 kcal/mol
Surface area19260 Å2
手法PISA
7
R: ACC1 Fab fragment heavy chain
S: ACC1 Fab fragment light chain
T: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,3053
ポリマ－50,3053
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-28 kcal/mol
Surface area19830 Å2
手法PISA
8
U: ACC1 Fab fragment heavy chain
V: ACC1 Fab fragment light chain
W: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)50,0913
ポリマ－50,0913
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-27 kcal/mol
Surface area19530 Å2
手法PISA
単位格子
Length a, b, c (Å)148.286, 155.099, 156.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21C
12A
22F
13A
23I
14A
24L
15A
25O
16A
26R
17A
27U
18B
28D
19B
29G
110B
210J
111B
211M
112B
212P
113B
213S
114B
214V
115C
215F
116C
216I
117C
217L
118C
218O
119C
219R
120C
220U
121D
221G
122D
222J
123D
223M
124D
224P
125D
225S
126D
226V
127F
227I
128F
228L
129F
229O
130F
230R
131F
231U
132G
232J
133G
233M
134G
234P
135G
235S
136G
236V
137I
237L
138I
238O
139I
239R
140I
240U
141J
241M
142J
242P
143J
243S
144J
244V
145L
245O
146L
246R
147L
247U
148M
248P
149M
249S
150M
250V
151O
251R
152O
252U
153P
253S
154P
254V
155R
255U
156S
256V

NCSドメイン領域:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA1 - 2181 - 218
21GLUGLUPROPROCD1 - 2181 - 218
12GLUGLUPROPROAA1 - 2181 - 218
22GLUGLUPROPROFG1 - 2181 - 218
13GLUGLUPROPROAA1 - 2181 - 218
23GLUGLUPROPROIJ1 - 2181 - 218
14GLUGLUPROPROAA1 - 2181 - 218
24GLUGLUPROPROLM1 - 2181 - 218
15GLUGLUPROPROAA1 - 2181 - 218
25GLUGLUPROPROOP1 - 2181 - 218
16GLUGLUGLYGLYAA1 - 2171 - 217
26GLUGLUGLYGLYRS1 - 2171 - 217
17GLUGLUPROPROAA1 - 2181 - 218
27GLUGLUPROPROUV1 - 2181 - 218
18ASPASPGLUGLUBB1 - 2171 - 217
28ASPASPGLUGLUDE1 - 2171 - 217
19ASPASPGLUGLUBB1 - 2171 - 217
29ASPASPGLUGLUGH1 - 2171 - 217
110ASPASPGLUGLUBB1 - 2171 - 217
210ASPASPGLUGLUJK1 - 2171 - 217
111ASPASPGLUGLUBB1 - 2171 - 217
211ASPASPGLUGLUMN1 - 2171 - 217
112ASPASPGLUGLUBB1 - 2171 - 217
212ASPASPGLUGLUPQ1 - 2171 - 217
113ASPASPGLUGLUBB1 - 2171 - 217
213ASPASPGLUGLUST1 - 2171 - 217
114ASPASPGLUGLUBB1 - 2171 - 217
214ASPASPGLUGLUVW1 - 2171 - 217
115GLUGLUGLYGLYCD1 - 2171 - 217
215GLUGLUGLYGLYFG1 - 2171 - 217
116GLUGLUPROPROCD1 - 2181 - 218
216GLUGLUPROPROIJ1 - 2181 - 218
117GLUGLUPROPROCD1 - 2181 - 218
217GLUGLUPROPROLM1 - 2181 - 218
118GLUGLUPROPROCD1 - 2181 - 218
218GLUGLUPROPROOP1 - 2181 - 218
119GLUGLUPROPROCD1 - 2181 - 218
219GLUGLUPROPRORS1 - 2181 - 218
120GLUGLUPROPROCD1 - 2181 - 218
220GLUGLUPROPROUV1 - 2181 - 218
121ASPASPGLUGLUDE1 - 2171 - 217
221ASPASPGLUGLUGH1 - 2171 - 217
122ASPASPGLUGLUDE1 - 2171 - 217
222ASPASPGLUGLUJK1 - 2171 - 217
123ASPASPGLUGLUDE1 - 2171 - 217
223ASPASPGLUGLUMN1 - 2171 - 217
124ASPASPGLUGLUDE1 - 2171 - 217
224ASPASPGLUGLUPQ1 - 2171 - 217
125ASPASPGLUGLUDE1 - 2171 - 217
225ASPASPGLUGLUST1 - 2171 - 217
126ASPASPGLUGLUDE1 - 2171 - 217
226ASPASPGLUGLUVW1 - 2171 - 217
127GLUGLUPROPROFG1 - 2181 - 218
227GLUGLUPROPROIJ1 - 2181 - 218
128GLUGLUGLYGLYFG1 - 2171 - 217
228GLUGLUGLYGLYLM1 - 2171 - 217
129GLUGLUPROPROFG1 - 2181 - 218
229GLUGLUPROPROOP1 - 2181 - 218
130GLUGLUILEILEFG1 - 2201 - 220
230GLUGLUILEILERS1 - 2201 - 220
131GLUGLUPROPROFG1 - 2181 - 218
231GLUGLUPROPROUV1 - 2181 - 218
132ASPASPGLUGLUGH1 - 2171 - 217
232ASPASPGLUGLUJK1 - 2171 - 217
133ASPASPGLUGLUGH1 - 2171 - 217
233ASPASPGLUGLUMN1 - 2171 - 217
134ASPASPGLUGLUGH1 - 2171 - 217
234ASPASPGLUGLUPQ1 - 2171 - 217
135ASPASPGLUGLUGH1 - 2171 - 217
235ASPASPGLUGLUST1 - 2171 - 217
136ASPASPGLUGLUGH1 - 2171 - 217
236ASPASPGLUGLUVW1 - 2171 - 217
137GLUGLUPROPROIJ1 - 2181 - 218
237GLUGLUPROPROLM1 - 2181 - 218
138GLUGLUPROPROIJ1 - 2181 - 218
238GLUGLUPROPROOP1 - 2181 - 218
139GLUGLUGLYGLYIJ1 - 2171 - 217
239GLUGLUGLYGLYRS1 - 2171 - 217
140GLUGLUPROPROIJ1 - 2181 - 218
240GLUGLUPROPROUV1 - 2181 - 218
141ASPASPGLUGLUJK1 - 2171 - 217
241ASPASPGLUGLUMN1 - 2171 - 217
142ASPASPGLUGLUJK1 - 2171 - 217
242ASPASPGLUGLUPQ1 - 2171 - 217
143ASPASPGLUGLUJK1 - 2171 - 217
243ASPASPGLUGLUST1 - 2171 - 217
144ASPASPGLUGLUJK1 - 2171 - 217
244ASPASPGLUGLUVW1 - 2171 - 217
145GLUGLUPROPROLM1 - 2181 - 218
245GLUGLUPROPROOP1 - 2181 - 218
146GLUGLUPROPROLM1 - 2181 - 218
246GLUGLUPROPRORS1 - 2181 - 218
147GLUGLUPROPROLM1 - 2181 - 218
247GLUGLUPROPROUV1 - 2181 - 218
148ASPASPGLUGLUMN1 - 2171 - 217
248ASPASPGLUGLUPQ1 - 2171 - 217
149ASPASPGLUGLUMN1 - 2171 - 217
249ASPASPGLUGLUST1 - 2171 - 217
150ASPASPGLUGLUMN1 - 2171 - 217
250ASPASPGLUGLUVW1 - 2171 - 217
151GLUGLUPROPROOP1 - 2181 - 218
251GLUGLUPROPRORS1 - 2181 - 218
152GLUGLUPROPROOP1 - 2181 - 218
252GLUGLUPROPROUV1 - 2181 - 218
153ASPASPGLUGLUPQ1 - 2171 - 217
253ASPASPGLUGLUST1 - 2171 - 217
154ASPASPGLUGLUPQ1 - 2171 - 217
254ASPASPGLUGLUVW1 - 2171 - 217
155GLUGLUGLYGLYRS1 - 2171 - 217
255GLUGLUGLYGLYUV1 - 2171 - 217
156ASPASPGLUGLUST1 - 2171 - 217
256ASPASPGLUGLUVW1 - 2171 - 217

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56

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要素

#1: 抗体
ACC1 Fab fragment heavy chain


分子量: 23353.164 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: B cell hybridoma / 株: B10.RIII.Cia5
#2: 抗体
ACC1 Fab fragment light chain


分子量: 23721.199 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: B cell hybridoma / 株: B10.RIII.Cia5
#3: タンパク質・ペプチド
triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II / Alpha-1 type II collagen


分子量: 3016.176 Da / 分子数: 8 / 由来タイプ: 合成
詳細: the synthesized peptide is homotrimeric and triple-helical in solution, but bound as single alpha-chain to the ACC1 Fab fragment
由来: (合成) Mus musculus (ハツカネズミ) / 参照: UniProt: P28481
#4: 抗体 ACC1 Fab fragment heavy chain


分子量: 23567.428 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: B cell hybridoma / 株: B10.RIII.Cia5

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.24 Å3/Da / 溶媒含有率: 45.08 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 20% (w/v) PEG 3350, 0.1 M Bistris-Propane pH 6.5, 0.2 M NaBr

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.9763 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年5月10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: 0.9763 Å / 相対比: 1
反射解像度: 3.1→78.14 Å / Num. obs: 65914 / % possible obs: 100 % / 冗長度: 4.7 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.1
反射 シェル解像度: 3.1→3.17 Å / 冗長度: 4.8 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4370 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0155精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5MU0

5mu0


解像度: 3.1→78.14 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.873 / SU B: 69.143 / SU ML: 0.492 / 交差検証法: THROUGHOUT / ESU R Free: 0.545 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.26396 3245 4.9 %RANDOM
Rwork0.23133 ---
obs0.23296 62669 99.84 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 74.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1.78 Å2-0 Å2
3----1.31 Å2
精密化ステップサイクル: 1 / 解像度: 3.1→78.14 Å
タンパク質核酸リガンド溶媒全体
原子数26877 0 0 0 26877
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227531
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225180
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.94737407
X-RAY DIFFRACTIONr_angle_other_deg1.646358309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98553516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27524.4441080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.813154342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12915112
X-RAY DIFFRACTIONr_chiral_restr0.1150.24199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02131047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026121
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1453.92514154
X-RAY DIFFRACTIONr_mcbond_other1.1453.92514154
X-RAY DIFFRACTIONr_mcangle_it1.9915.88717640
X-RAY DIFFRACTIONr_mcangle_other1.9915.88717641
X-RAY DIFFRACTIONr_scbond_it0.9923.97213377
X-RAY DIFFRACTIONr_scbond_other0.9923.97213377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7265.92419768
X-RAY DIFFRACTIONr_long_range_B_refined3.09844.11528159
X-RAY DIFFRACTIONr_long_range_B_other3.09844.11528160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / タイプ: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-ID数Rms dev position (Å)
11A130760.06
12C130760.06
21A130600.05
22F130600.05
31A131580.05
32I131580.05
41A130780.05
42L130780.05
51A129640.05
52O129640.05
61A130440.06
62R130440.06
71A130520.07
72U130520.07
81B133740.05
82D133740.05
91B134320.05
92G134320.05
101B135180.03
102J135180.03
111B134320.05
112M134320.05
121B133480.06
122P133480.06
131B134080.05
132S134080.05
141B134420.04
142V134420.04
151C129500.06
152F129500.06
161C131020.05
162I131020.05
171C130280.06
172L130280.06
181C129580.05
182O129580.05
191C130000.06
192R130000.06
201C129920.07
202U129920.07
211D133080.06
212G133080.06
221D133280.05
222J133280.05
231D133640.06
232M133640.06
241D132680.07
242P132680.07
251D133300.06
252S133300.06
261D132460.06
262V132460.06
271F130520.05
272I130520.05
281F129980.06
282L129980.06
291F129880.05
292O129880.05
301F132380.04
302R132380.04
311F131200.06
312U131200.06
321G134290.05
322J134290.05
331G133510.06
332M133510.06
341G133290.07
342P133290.07
351G133530.06
352S133530.06
361G132790.06
362V132790.06
371I130400.06
372L130400.06
381I130420.04
382O130420.04
391I130180.06
392R130180.06
401I130580.07
402U130580.07
411J133640.05
412M133640.05
421J133460.06
422P133460.06
431J133660.06
432S133660.06
441J133760.05
442V133760.05
451L130220.05
452O130220.05
461L131100.06
462R131100.06
471L130540.07
472U130540.07
481M133020.06
482P133020.06
491M133760.06
492S133760.06
501M132740.06
502V132740.06
511O129760.05
512R129760.05
521O129900.05
522U129900.05
531P133520.07
532S133520.07
541P132060.07
542V132060.07
551R131660.06
552U131660.06
561S132320.06
562V132320.06
LS精密化 シェル解像度: 3.1→3.18 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.367 221 -
Rwork0.321 4582 -
obs--99.96 %
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)
11.9632-0.7469-0.37474.95731.74721.7169-0.2201-0.2369-0.21780.10570.05660.17350.29390.31150.16350.09980.04120.03240.20740.07810.0415-6.8006-40.390636.03
21.67580.1019-0.25684.36510.52872.4274-0.12640.2224-0.1376-0.42890.104-0.14970.17550.46020.02240.07930.05970.04040.32160.03520.03933.1431-38.759520.5693
314.7175.4889-5.3323.7149-0.91632.623-0.0688-0.68850.0863-0.08290.352-0.383-0.00810.6295-0.28320.35870.0735-0.08380.5107-0.1180.44814.5296-15.644443.557
40.2927-0.14780.08584.8974-2.95893.66480.0234-0.042-0.0713-0.12590.19990.72430.0033-0.4689-0.22340.0604-0.00780.0360.213-0.10130.5496-40.706-15.461643.6939
51.28890.9729-0.04415.1072-1.39712.66410.0415-0.0020.20050.4344-0.05560.0029-0.04360.37310.01420.11970.00350.09580.1915-0.08540.2185-24.2038-18.670251.2736
62.0054-0.28243.056917.9276-2.11934.8225-0.20460.05510.3803-0.6452-0.3552-0.1458-0.22190.13220.55980.4120.1015-0.0780.3705-0.04730.5505-30.59229.288236.5748
72.34740.5467-2.36360.8391-0.73544.14820.1964-0.01230.2996-0.03210.0110.0873-0.45490.1554-0.20740.17770.0075-0.06780.1881-0.12350.3221-61.5693-45.701831.4534
81.86660.709-1.40492.9502-1.56253.88930.03470.0151-0.1934-0.0334-0.1817-0.03490.13130.53140.1470.09850.1245-0.08820.2655-0.09470.1018-51.0887-60.285727.9926
93.3915-1.942-5.98821.14473.427410.7052-0.4883-0.1966-0.36870.2844-0.0220.24560.63930.42420.51030.5674-0.16440.06930.6093-0.10750.5812-79.4235-64.641742.7227
104.0439-0.07770.85461.8193-0.2021.60020.09080.1829-0.0311-0.167-0.1693-0.09840.03720.22550.07860.16530.10110.04630.11760.03170.0206-23.5954-67.910744.0494
114.32330.25540.4171.8369-0.52492.5395-0.0818-0.2243-0.21990.30950.0285-0.09040.120.30720.05330.20690.13550.03680.12690.04610.0286-22.3605-74.829860.9198
128.0443-3.0572-4.663919.28852.19222.75440.27160.20680.2405-0.642-0.02640.4454-0.1254-0.2238-0.24510.5804-0.1391-0.23260.6220.07640.5503-45.2073-85.775540.4844
136.17880.025-2.74771.0243-0.83682.2337-0.37830.9567-0.2819-0.37770.07160.20870.6356-0.57780.30670.689-0.20660.04470.4128-0.08270.4247-46.7377-11.88031.0859
145.87781.3303-1.66292.9709-0.56811.8702-0.186-0.33160.4763-0.01550.14530.16770.0586-0.0260.04070.3520.0993-0.05060.20880.00930.2936-48.5636-2.00616.675
1513.7498-6.8227-6.30017.34427.3527.4018-0.7851-0.5744-0.71560.06780.8688-0.009-0.00930.9065-0.08370.5214-0.05640.09860.42420.09920.6162-26.0035.6841-5.1029
162.3683-1.1312-1.78414.35262.63.907-0.0326-0.85840.36990.09890.3656-0.3362-0.16261.0305-0.3330.1164-0.00440.02430.583-0.00510.1504-32.0814-58.883987.2384
173.2120.3878-0.63074.08452.30573.7549-0.0213-0.41020.2602-0.02330.10360.2802-0.33040.2684-0.08230.16330.03920.0690.30940.09220.1653-49.5013-55.409192.773
185.7540.0694-8.98542.05393.60520.8903-0.26620.40610.2314-0.14950.22610.3743-0.0193-0.18680.04010.56520.02660.13550.2776-0.03880.6647-41.1376-83.834380.9983
191.6739-0.98080.99664.0171-2.27662.3683-0.12280.00840.29810.126-0.0479-0.017-0.4843-0.11150.17060.24790.0260.03460.2282-0.08210.2086-69.9463-35.790674.5587
201.6654-0.35370.41254.4762-0.86242.34380.06730.33840.0042-0.5312-0.13870.0432-0.0503-0.20960.07140.13350.09230.01840.2902-0.08440.1526-78.1951-41.180459.1903
2110.48956.53211.42345.81671.75820.62880.2146-1.36140.05240.3461-0.38030.39290.13590.03460.16580.3297-0.0002-0.02370.65810.24440.5633-77.8264-62.247284.3369
224.16461.53032.59651.28590.93614.26580.41550.3044-0.6333-0.0059-0.15240.14080.5564-0.0796-0.26310.25520.018-0.05790.4089-0.090.3957-12.6793-36.2925-6.4442
234.29111.30311.59862.2580.89912.33910.08520.64410.263-0.0965-0.13530.2447-0.3758-0.29220.05010.34450.08620.04350.61380.0090.1887-21.0879-21.679-13.6094
241.60260.4782-1.6920.45940.65816.84570.0965-0.67790.15710.3165-0.3512-0.01480.7511-0.12890.25470.57580.0271-0.08940.6308-0.15230.66167.6724-18.59620.8358
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2B1 - 217
3X-RAY DIFFRACTION3X11 - 21
4X-RAY DIFFRACTION4C1 - 218
5X-RAY DIFFRACTION5D1 - 217
6X-RAY DIFFRACTION6E13 - 21
7X-RAY DIFFRACTION7F1 - 220
8X-RAY DIFFRACTION8G1 - 217
9X-RAY DIFFRACTION9H13 - 21
10X-RAY DIFFRACTION10I1 - 218
11X-RAY DIFFRACTION11J1 - 217
12X-RAY DIFFRACTION12K13 - 22
13X-RAY DIFFRACTION13L1 - 218
14X-RAY DIFFRACTION14M1 - 217
15X-RAY DIFFRACTION15N13 - 21
16X-RAY DIFFRACTION16O1 - 218
17X-RAY DIFFRACTION17P1 - 217
18X-RAY DIFFRACTION18Q14 - 21
19X-RAY DIFFRACTION19R1 - 220
20X-RAY DIFFRACTION20S1 - 217
21X-RAY DIFFRACTION21T10 - 21
22X-RAY DIFFRACTION22U1 - 218
23X-RAY DIFFRACTION23V1 - 217
24X-RAY DIFFRACTION24W13 - 21

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万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.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

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