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- PDB-7yq2: Crystal structure of photosystem II expressing psbA2 gene only -

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基本情報

登録情報
データベース: PDB / ID: 7yq2
タイトルCrystal structure of photosystem II expressing psbA2 gene only
要素
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
キーワードPHOTOSYNTHESIS / ELECTRON TRANSPORT
機能・相同性
機能・相同性情報


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
類似検索 - 分子機能
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
類似検索 - ドメイン・相同性
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Unknown ligand / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 2 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Y / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
類似検索 - 構成要素
生物種Thermosynechococcus vestitus BP-1 (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 Å
データ登録者Nakajima, Y. / Suga, M. / Shen, J.R.
資金援助 日本, 1件
組織認可番号国
Japan Society for the Promotion of Science (JSPS)20H03226 日本
引用ジャーナル: J.Biol.Chem. / 年: 2022
タイトル: Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit.
著者: Nakajima, Y. / Ugai-Amo, N. / Tone, N. / Nakagawa, A. / Iwai, M. / Ikeuchi, M. / Sugiura, M. / Suga, M. / Shen, J.R.
履歴
登録2022年8月5日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年11月30日Provider: repository / タイプ: Initial release
改定 1.12022年12月7日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Photosystem II protein D1 2
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1 2
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)793,817453
ポリマ－630,11239
非ポリマー163,705414
水61,6113420
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)122.135, 228.172, 286.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 11 through 24 or resid 26...
21(chain a and ((resid 11 and (name CA or name...
12(chain B and (resid 2 through 35 or resid 37...
22(chain b and (resid 2 through 35 or resid 37...
13(chain C and (resid 23 through 134 or resid 136...
23(chain c and (resid 23 through 134 or resid 136...
14(chain D and (resid 11 through 125 or resid 127...
24(chain d and ((resid 11 through 12 and (name N...
15(chain E and (resid 6 or resid 8 through 11...
25(chain e and (resid 6 or resid 8 through 11...
16(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))
26(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))
17(chain H and (resid 2 or resid 4 through 201))
27(chain h and (resid 2 or resid 4 through 62...
18(chain I and (resid 1 or (resid 2 and (name...
28(chain i and (resid 1 through 37 or (resid 101...
19(chain J and (resid 5 through 40 or resid 101...
29(chain j and (resid 5 through 40 or resid 101 through 103))
110chain K
210chain k
111(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))
211(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))
112(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))
212(chain m and (resid 1 through 15 or resid 17...
113(chain O and (resid 4 through 48 or resid 50...
213(chain o and (resid 4 through 48 or resid 50...
114(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))
214(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))
115(chain U and resid 8 through 104)
215(chain u and ((resid 8 and (name N or name...
116(chain V and (resid 1 or resid 3 through 14...
216(chain v and (resid 1 or resid 3 through 14...
117(chain X and resid 2 through 40)
217(chain x and (resid 2 through 37 or (resid 38...
118(chain Y and (resid 17 through 29 or resid 31 through 46))
218(chain y and (resid 17 through 29 or resid 31...
119(chain Z and (resid 1 through 2 or (resid 3...
219(chain z and (resid 1 through 33 or (resid 34...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 11 through 24 or resid 26...A11 - 24
121(chain A and (resid 11 through 24 or resid 26...A26 - 67
131(chain A and (resid 11 through 24 or resid 26...A69 - 220
141(chain A and (resid 11 through 24 or resid 26...A222 - 228
151(chain A and (resid 11 through 24 or resid 26...A229
161(chain A and (resid 11 through 24 or resid 26...A11 - 344
171(chain A and (resid 11 through 24 or resid 26...A11 - 344
181(chain A and (resid 11 through 24 or resid 26...A11 - 344
191(chain A and (resid 11 through 24 or resid 26...A11 - 344
211(chain a and ((resid 11 and (name CA or name...a11
221(chain a and ((resid 11 and (name CA or name...a9 - 344
231(chain a and ((resid 11 and (name CA or name...a9 - 344
112(chain B and (resid 2 through 35 or resid 37...B2 - 35
122(chain B and (resid 2 through 35 or resid 37...B37 - 75
132(chain B and (resid 2 through 35 or resid 37...B77 - 120
142(chain B and (resid 2 through 35 or resid 37...B122 - 126
152(chain B and (resid 2 through 35 or resid 37...B127
162(chain B and (resid 2 through 35 or resid 37...B2 - 506
172(chain B and (resid 2 through 35 or resid 37...B2 - 506
182(chain B and (resid 2 through 35 or resid 37...B2 - 506
192(chain B and (resid 2 through 35 or resid 37...B2 - 506
212(chain b and (resid 2 through 35 or resid 37...b2 - 35
222(chain b and (resid 2 through 35 or resid 37...b37 - 75
232(chain b and (resid 2 through 35 or resid 37...b77 - 120
242(chain b and (resid 2 through 35 or resid 37...b122 - 147
252(chain b and (resid 2 through 35 or resid 37...b0
262(chain b and (resid 2 through 35 or resid 37...b2 - 505
272(chain b and (resid 2 through 35 or resid 37...b2 - 505
282(chain b and (resid 2 through 35 or resid 37...b2 - 505
292(chain b and (resid 2 through 35 or resid 37...b2 - 505
2102(chain b and (resid 2 through 35 or resid 37...b2 - 505
113(chain C and (resid 23 through 134 or resid 136...C23 - 134
123(chain C and (resid 23 through 134 or resid 136...C136 - 144
133(chain C and (resid 23 through 134 or resid 136...C146 - 200
143(chain C and (resid 23 through 134 or resid 136...C202 - 212
153(chain C and (resid 23 through 134 or resid 136...C214 - 377
163(chain C and (resid 23 through 134 or resid 136...C379 - 415
173(chain C and (resid 23 through 134 or resid 136...C417 - 470
183(chain C and (resid 23 through 134 or resid 136...C472 - 473
193(chain C and (resid 23 through 134 or resid 136...C502 - 513
1103(chain C and (resid 23 through 134 or resid 136...C515
1113(chain C and (resid 23 through 134 or resid 136...C517 - 518
213(chain c and (resid 23 through 134 or resid 136...c23 - 134
223(chain c and (resid 23 through 134 or resid 136...c136 - 144
233(chain c and (resid 23 through 134 or resid 136...c146 - 200
243(chain c and (resid 23 through 134 or resid 136...c202 - 212
253(chain c and (resid 23 through 134 or resid 136...c379 - 415
263(chain c and (resid 23 through 134 or resid 136...c472 - 913
273(chain c and (resid 23 through 134 or resid 136...c912
283(chain c and (resid 23 through 134 or resid 136...c917 - 918
114(chain D and (resid 11 through 125 or resid 127...D11 - 125
124(chain D and (resid 11 through 125 or resid 127...D127 - 232
134(chain D and (resid 11 through 125 or resid 127...D233 - 234
144(chain D and (resid 11 through 125 or resid 127...D11 - 352
154(chain D and (resid 11 through 125 or resid 127...D11 - 352
164(chain D and (resid 11 through 125 or resid 127...D11 - 352
174(chain D and (resid 11 through 125 or resid 127...D11 - 352
214(chain d and ((resid 11 through 12 and (name N...d11 - 12
224(chain d and ((resid 11 through 12 and (name N...d11 - 352
234(chain d and ((resid 11 through 12 and (name N...d11 - 352
244(chain d and ((resid 11 through 12 and (name N...d11 - 352
254(chain d and ((resid 11 through 12 and (name N...d11 - 352
115(chain E and (resid 6 or resid 8 through 11...E6
125(chain E and (resid 6 or resid 8 through 11...E8 - 11
135(chain E and (resid 6 or resid 8 through 11...E13 - 58
145(chain E and (resid 6 or resid 8 through 11...E59 - 60
155(chain E and (resid 6 or resid 8 through 11...E3 - 201
165(chain E and (resid 6 or resid 8 through 11...E3 - 201
175(chain E and (resid 6 or resid 8 through 11...E3 - 201
215(chain e and (resid 6 or resid 8 through 11...e6
225(chain e and (resid 6 or resid 8 through 11...e8 - 11
235(chain e and (resid 6 or resid 8 through 11...e13 - 59
245(chain e and (resid 6 or resid 8 through 11...e60
255(chain e and (resid 6 or resid 8 through 11...e6 - 84
265(chain e and (resid 6 or resid 8 through 11...e6 - 84
275(chain e and (resid 6 or resid 8 through 11...e6 - 84
285(chain e and (resid 6 or resid 8 through 11...e6 - 84
116(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F14 - 43
126(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F45
136(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F101
146(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F103
216(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f14 - 43
226(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f45
236(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f101
246(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f103
117(chain H and (resid 2 or resid 4 through 201))H0
217(chain h and (resid 2 or resid 4 through 62...h2
227(chain h and (resid 2 or resid 4 through 62...h4 - 62
237(chain h and (resid 2 or resid 4 through 62...h63
247(chain h and (resid 2 or resid 4 through 62...h2 - 66
257(chain h and (resid 2 or resid 4 through 62...h2 - 66
267(chain h and (resid 2 or resid 4 through 62...h2 - 66
277(chain h and (resid 2 or resid 4 through 62...h2 - 66
287(chain h and (resid 2 or resid 4 through 62...h2 - 66
118(chain I and (resid 1 or (resid 2 and (name...I1
128(chain I and (resid 1 or (resid 2 and (name...I2
138(chain I and (resid 1 or (resid 2 and (name...I1 - 37
148(chain I and (resid 1 or (resid 2 and (name...I1 - 37
158(chain I and (resid 1 or (resid 2 and (name...I1 - 37
168(chain I and (resid 1 or (resid 2 and (name...I1 - 37
218(chain i and (resid 1 through 37 or (resid 101...i0
119(chain J and (resid 5 through 40 or resid 101...J5 - 40
129(chain J and (resid 5 through 40 or resid 101...J101 - 102
139(chain J and (resid 5 through 40 or resid 101...J103
149(chain J and (resid 5 through 40 or resid 101...J5 - 40
159(chain J and (resid 5 through 40 or resid 101...J5 - 40
169(chain J and (resid 5 through 40 or resid 101...J5 - 40
179(chain J and (resid 5 through 40 or resid 101...J5 - 40
189(chain J and (resid 5 through 40 or resid 101...J5 - 40
219(chain j and (resid 5 through 40 or resid 101 through 103))j5 - 40
229(chain j and (resid 5 through 40 or resid 101 through 103))j101 - 103
1110chain KK10 - 46
2110chain kk10 - 46
1111(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L1 - 7
1211(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L9 - 23
1311(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L25 - 37
1411(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L101
2111(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l1 - 7
2211(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l9 - 23
2311(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l25 - 37
2411(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l101
1112(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))M1 - 15
1212(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))M17 - 34
1312(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))M101 - 102
2112(chain m and (resid 1 through 15 or resid 17...m1 - 15
2212(chain m and (resid 1 through 15 or resid 17...m17 - 32
2312(chain m and (resid 1 through 15 or resid 17...m33
2412(chain m and (resid 1 through 15 or resid 17...m1 - 34
2512(chain m and (resid 1 through 15 or resid 17...m34
2612(chain m and (resid 1 through 15 or resid 17...m1 - 34
1113(chain O and (resid 4 through 48 or resid 50...O4 - 48
1213(chain O and (resid 4 through 48 or resid 50...O50 - 68
1313(chain O and (resid 4 through 48 or resid 50...O70 - 73
1413(chain O and (resid 4 through 48 or resid 50...O75
1513(chain O and (resid 4 through 48 or resid 50...O100 - 17190
1613(chain O and (resid 4 through 48 or resid 50...O1919795
1713(chain O and (resid 4 through 48 or resid 50...O197 - 216
1813(chain O and (resid 4 through 48 or resid 50...O2 - 216
1913(chain O and (resid 4 through 48 or resid 50...O218 - 246
11013(chain O and (resid 4 through 48 or resid 50...O301
2113(chain o and (resid 4 through 48 or resid 50...o4 - 48
2213(chain o and (resid 4 through 48 or resid 50...o50 - 61
2313(chain o and (resid 4 through 48 or resid 50...o62 - 63
2413(chain o and (resid 4 through 48 or resid 50...o4 - 246
2513(chain o and (resid 4 through 48 or resid 50...o4 - 246
2613(chain o and (resid 4 through 48 or resid 50...o4 - 246
2713(chain o and (resid 4 through 48 or resid 50...o4 - 246
1114(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))T1 - 24
1214(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))T26 - 30
1314(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))T101
2114(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))t1 - 24
2214(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))t26 - 30
2314(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))t101
1115(chain U and resid 8 through 104)U8 - 104
2115(chain u and ((resid 8 and (name N or name...u8
2215(chain u and ((resid 8 and (name N or name...u8 - 104
2315(chain u and ((resid 8 and (name N or name...u8 - 104
2415(chain u and ((resid 8 and (name N or name...u8 - 104
2515(chain u and ((resid 8 and (name N or name...u8 - 104
1116(chain V and (resid 1 or resid 3 through 14...V1
1216(chain V and (resid 1 or resid 3 through 14...V3 - 14
1316(chain V and (resid 1 or resid 3 through 14...V16
1416(chain V and (resid 1 or resid 3 through 14...V17
1516(chain V and (resid 1 or resid 3 through 14...V1 - 137
1616(chain V and (resid 1 or resid 3 through 14...V1 - 137
1716(chain V and (resid 1 or resid 3 through 14...V1 - 137
2116(chain v and (resid 1 or resid 3 through 14...v1
2216(chain v and (resid 1 or resid 3 through 14...v3 - 14
2316(chain v and (resid 1 or resid 3 through 14...v16 - 54
2416(chain v and (resid 1 or resid 3 through 14...v56 - 105
2516(chain v and (resid 1 or resid 3 through 14...v107 - 137
2616(chain v and (resid 1 or resid 3 through 14...v201
1117(chain X and resid 2 through 40)X2 - 40
2117(chain x and (resid 2 through 37 or (resid 38...x2 - 37
2217(chain x and (resid 2 through 37 or (resid 38...x38
2317(chain x and (resid 2 through 37 or (resid 38...x2 - 40
2417(chain x and (resid 2 through 37 or (resid 38...x2 - 40
2517(chain x and (resid 2 through 37 or (resid 38...x2 - 40
2617(chain x and (resid 2 through 37 or (resid 38...x2 - 40
1118(chain Y and (resid 17 through 29 or resid 31 through 46))Y17 - 29
1218(chain Y and (resid 17 through 29 or resid 31 through 46))Y31 - 46
2118(chain y and (resid 17 through 29 or resid 31...y17 - 29
2218(chain y and (resid 17 through 29 or resid 31...y31 - 42
2318(chain y and (resid 17 through 29 or resid 31...y43
2418(chain y and (resid 17 through 29 or resid 31...y17 - 46
2518(chain y and (resid 17 through 29 or resid 31...y17 - 46
2618(chain y and (resid 17 through 29 or resid 31...y17 - 46
2718(chain y and (resid 17 through 29 or resid 31...y17 - 46
1119(chain Z and (resid 1 through 2 or (resid 3...Z1 - 2
1219(chain Z and (resid 1 through 2 or (resid 3...Z3
1319(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
1419(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
1519(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
1619(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
2119(chain z and (resid 1 through 33 or (resid 34...z1 - 33
2219(chain z and (resid 1 through 33 or (resid 34...z34 - 35
2319(chain z and (resid 1 through 33 or (resid 34...z1 - 62
2419(chain z and (resid 1 through 33 or (resid 34...z1 - 62
2519(chain z and (resid 1 through 33 or (resid 34...z1 - 62
2619(chain z and (resid 1 through 33 or (resid 34...z1 - 62

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

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要素

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Photosystem II ... , 17種, 33分子 AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...

#1: タンパク質 Photosystem II protein D1 2 / PSII D1 protein 2 / Photosystem II Q(B) protein 2


分子量: 39762.492 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: P0A446, photosystem II
#2: タンパク質 Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


分子量: 56656.457 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DIQ1
#3: タンパク質 Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


分子量: 50287.500 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DIF8
#4: タンパク質 Photosystem II D2 protein / PSII D2 protein / Photosystem II Q(A) protein


分子量: 39388.156 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8CM25, photosystem II
#7: タンパク質 Photosystem II reaction center protein H / PSII-H


分子量: 7358.754 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DJ43
#8: タンパク質・ペプチド Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


分子量: 4438.255 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DJZ6
#9: タンパク質・ペプチド Photosystem II reaction center protein J / PSII-J


分子量: 4105.908 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: P59087
#10: タンパク質・ペプチド Photosystem II reaction center protein K / PSII-K


分子量: 5028.083 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q9F1K9
#11: タンパク質・ペプチド Photosystem II reaction center protein L / PSII-L


分子量: 4299.044 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DIN8
#12: タンパク質・ペプチド Photosystem II reaction center protein M / PSII-M


分子量: 4009.682 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DHA7
#13: タンパク質 Photosystem II manganese-stabilizing polypeptide / MSP


分子量: 29637.443 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: P0A431
#14: タンパク質・ペプチド Photosystem II reaction center protein T / PSII-T / PSII-Tc


分子量: 3906.738 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DIQ0
#15: タンパク質 Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


分子量: 15030.986 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q9F1L5
#17: タンパク質・ペプチド Photosystem II reaction center protein Ycf12


分子量: 5039.143 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DJI1
#18: タンパク質・ペプチド Photosystem II reaction center X protein


分子量: 4322.226 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q9F1R6
#19: タンパク質 Photosystem II reaction center protein Z / PSII-Z


分子量: 6794.197 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DHJ2
#20: タンパク質・ペプチド Photosystem II protein Y


分子量: 4590.648 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DKM3

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Cytochrome b559 subunit ... , 2種, 4分子 EeFf

#5: タンパク質 Cytochrome b559 subunit alpha / PSII reaction center subunit V


分子量: 9580.840 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DIP0
#6: タンパク質・ペプチド Cytochrome b559 subunit beta / PSII reaction center subunit VI


分子量: 5067.900 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: Q8DIN9

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タンパク質 , 1種, 2分子 Vv

#16: タンパク質 Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


分子量: 18046.943 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermosynechococcus vestitus BP-1 (バクテリア)
参照: UniProt: P0A386

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糖 , 3種, 60分子

#31: 糖
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE / ドデシルβ-D-マルトシド


タイプ: D-saccharide / 分子量: 510.615 Da / 分子数: 19 / 由来タイプ: 合成 / 式: C24H46O11 / コメント: 可溶化剤*YM
#36: 糖...
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside / ヘプチル1-チオ-β-D-グルコピラノシド


タイプ: D-saccharide / 分子量: 294.408 Da / 分子数: 31 / 由来タイプ: 合成 / 式: C13H26O5S / コメント: 可溶化剤*YM
#37: 糖
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


タイプ: saccharide / 分子量: 949.299 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C51H96O15

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非ポリマー , 20種, 3774分子

#21: 化合物 ChemComp-OEX / CA-MN4-O5 CLUSTER


分子量: 339.827 Da / 分子数: 2 / 由来タイプ: 合成 / 式: CaMn4O5
#22: 化合物 ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe
#23: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#24: 化合物...
ChemComp-CLA / CHLOROPHYLL A


分子量: 893.489 Da / 分子数: 70 / 由来タイプ: 合成 / 式: C55H72MgN4O5
#25: 化合物
ChemComp-PHO / PHEOPHYTIN A / 132α-(メトキシカルボニル)-31,32-ジデヒ(以下略)


分子量: 871.200 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C55H74N4O5 / タイプ: SUBJECT OF INVESTIGATION
#26: 化合物
ChemComp-BCR / BETA-CAROTENE / β-カロチン


分子量: 536.873 Da / 分子数: 20 / 由来タイプ: 合成 / 式: C40H56
#27: 化合物
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL / (2S)-1-O,2-O-ジパルミトイル-3-O-(6-スルホ-6-デオキシ-α-D-グルコピラノシル)グリセロ-ル


分子量: 795.116 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C41H78O12S
#28: 化合物
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


分子量: 787.158 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C45H86O10
#29: 化合物
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


分子量: 749.201 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C53H80O2 / タイプ: SUBJECT OF INVESTIGATION
#30: 化合物...
ChemComp-UNL / UNKNOWN LIGAND


分子量: 258.120 Da / 分子数: 77 / 由来タイプ: 合成
#32: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C3H8O3
#33: 化合物 ChemComp-BCT / BICARBONATE ION / 炭酸水素アニオン


分子量: 61.017 Da / 分子数: 3 / 由来タイプ: 合成 / 式: CHO3 / コメント: pH緩衝剤*YM
#34: 化合物...
ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド


分子量: 78.133 Da / 分子数: 116 / 由来タイプ: 合成 / 式: C2H6OS / コメント: DMSO, 沈殿剤*YM
#35: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Ca
#38: 化合物
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ジパルミトイルホスファチジルグリセロ-ル


分子量: 722.970 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C38H75O10P / コメント: リン脂質*YM
#39: 化合物 ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#40: 化合物 ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin / β-クリプトキサンチン


分子量: 552.872 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C40H56O
#41: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#42: 化合物 ChemComp-HEC / HEME C


分子量: 618.503 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C34H34FeN4O4
#43: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3420 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかY

-
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: 3.21 Å3/Da / 溶媒含有率: 61.69 %
結晶化温度: 285 K / 手法: マイクロバッチ法 / pH: 6
詳細: 5% PEG 1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER, pH 6.0, MICRO-BATCH METHOD UNDER OIL, TEMPARATURE 285K

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SPring-8 / ビームライン: BL41XU / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2018年1月26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: 1 Å / 相対比: 1
反射解像度: 1.9→20 Å / Num. obs: 621644 / % possible obs: 99.6 % / 冗長度: 4.9 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.1 / Χ2: 0.855 / Net I/σ(I): 11.03
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.014.8071.2971.35955640.6611.45399.7
2.01-2.15.0240.82.3640890.8380.89199.8
2.1-2.34.8670.4933.81091880.9260.55199.8
2.3-2.54.9130.2886.3769980.9720.32199.8
2.5-34.9660.1411.461146500.9920.15699.8
3-44.940.05822.83915170.9980.06599.9
4-54.6850.03932.61327490.9980.04499.6

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
MOLREP位相決定
Cootモデル構築
PHENIX1.17.1_3660精密化
REFMAC5.8.0103精密化
精密化構造決定の手法: 分子置換
開始モデル: 3WU2

3wu2


解像度: 1.9→20 Å / SU ML: 0.19 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 20.93 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1844 31121 5.01 %
Rwork0.1512 590250 -
obs0.1528 621333 99.72 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 154.55 Å2 / Biso mean: 46.2203 Å2 / Biso min: 18.94 Å2
精密化ステップサイクル: final / 解像度: 1.9→20 Å
タンパク質核酸リガンド溶媒全体
原子数41169 0 10640 3468 55277
Biso mean--56.88 53.34 -
残基数----5302
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3073X-RAY DIFFRACTION11.22TORSIONAL
12a3073X-RAY DIFFRACTION11.22TORSIONAL
21B5814X-RAY DIFFRACTION11.22TORSIONAL
22b5814X-RAY DIFFRACTION11.22TORSIONAL
31C5157X-RAY DIFFRACTION11.22TORSIONAL
32c5157X-RAY DIFFRACTION11.22TORSIONAL
41D3292X-RAY DIFFRACTION11.22TORSIONAL
42d3292X-RAY DIFFRACTION11.22TORSIONAL
51E648X-RAY DIFFRACTION11.22TORSIONAL
52e648X-RAY DIFFRACTION11.22TORSIONAL
61F298X-RAY DIFFRACTION11.22TORSIONAL
62f298X-RAY DIFFRACTION11.22TORSIONAL
71H0X-RAY DIFFRACTION11.22TORSIONAL
72h0X-RAY DIFFRACTION11.22TORSIONAL
81I378X-RAY DIFFRACTION11.22TORSIONAL
82i378X-RAY DIFFRACTION11.22TORSIONAL
91J334X-RAY DIFFRACTION11.22TORSIONAL
92j334X-RAY DIFFRACTION11.22TORSIONAL
101K428X-RAY DIFFRACTION11.22TORSIONAL
102k428X-RAY DIFFRACTION11.22TORSIONAL
111L412X-RAY DIFFRACTION11.22TORSIONAL
112l412X-RAY DIFFRACTION11.22TORSIONAL
121M386X-RAY DIFFRACTION11.22TORSIONAL
122m386X-RAY DIFFRACTION11.22TORSIONAL
131O2156X-RAY DIFFRACTION11.22TORSIONAL
132o2156X-RAY DIFFRACTION11.22TORSIONAL
141T312X-RAY DIFFRACTION11.22TORSIONAL
142t312X-RAY DIFFRACTION11.22TORSIONAL
151U926X-RAY DIFFRACTION11.22TORSIONAL
152u926X-RAY DIFFRACTION11.22TORSIONAL
161V1256X-RAY DIFFRACTION11.22TORSIONAL
162v1256X-RAY DIFFRACTION11.22TORSIONAL
171X341X-RAY DIFFRACTION11.22TORSIONAL
172x341X-RAY DIFFRACTION11.22TORSIONAL
181Y250X-RAY DIFFRACTION11.22TORSIONAL
182y250X-RAY DIFFRACTION11.22TORSIONAL
191Z517X-RAY DIFFRACTION11.22TORSIONAL
192z517X-RAY DIFFRACTION11.22TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.920.32629960.30461929098
1.92-1.940.299810150.278319576100
1.94-1.970.296410510.267719521100
1.97-1.990.286110730.256619484100
1.99-2.020.288910560.247319503100
2.02-2.050.254610440.225219524100
2.05-2.080.247310280.212119626100
2.08-2.110.261710320.209219611100
2.11-2.140.24389840.200319585100
2.14-2.170.231410350.187919543100
2.17-2.210.22369960.183719630100
2.21-2.250.23119870.18519592100
2.25-2.30.21510180.17319654100
2.3-2.340.204410720.161419568100
2.34-2.390.199910210.153219649100
2.39-2.450.19319760.155219665100
2.45-2.510.186410440.146119625100
2.51-2.580.184310800.144619591100
2.58-2.650.184210300.143419695100
2.65-2.740.187610640.139619634100
2.74-2.840.183810040.138119745100
2.84-2.950.177110490.138819667100
2.95-3.080.189810260.138319807100
3.08-3.250.16510940.136119672100
3.25-3.450.163510470.129519775100
3.45-3.710.160510360.129119837100
3.71-4.080.159610550.125719844100
4.08-4.670.147410520.121719858100
4.67-5.860.160610420.131920073100
精密化 TLS手法: refined / Origin x: -13.169 Å / Origin y: -13.3638 Å / Origin z: 25.7906 Å
111213212223313233
T0.2693 Å20.0369 Å2-0.0141 Å2-0.2143 Å2-0.0305 Å2--0.1714 Å2
L0.129 °20.051 °2-0.0081 °2-0.2863 °2-0.1232 °2--0.3816 °2
S-0.0021 Å °0.0165 Å °-0.0075 Å °0.0042 Å °0.0397 Å °0.0156 Å °-0.0418 Å °0.0005 Å °-0.0371 Å °
精密化 TLSグループSelection details: all

+
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://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

+
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

+
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