[日本語] English
万見
- PDB-8dgw: Crystal structure of HCoV-HKU1 spike stem helix peptide in comple... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8dgw
タイトルCrystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent
要素
  • Antibody CC95.108 Fab heavy chain
  • Antibody CC95.108 Fab light chain
  • Spike protein S2'
キーワードIMMUNE SYSTEM / broadly / neutralizing / antibody / pan-betacoronavirus / S2 stem helix / spike / SARS-CoV-2 / MERS-CoV / HCoV-HKU1 / sarbecovirus / cross-reactive / cross-neutralizing
機能・相同性
機能・相同性情報


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human coronavirus HKU1 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.81 Å
データ登録者Liu, H. / Wilson, I.A.
資金援助 米国, 1件
組織認可番号国
Bill & Melinda Gates FoundationINV-004923 米国
引用ジャーナル: Immunity / 年: 2023
タイトル: Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.
著者: Zhou, P. / Song, G. / Liu, H. / Yuan, M. / He, W.T. / Beutler, N. / Zhu, X. / Tse, L.V. / Martinez, D.R. / Schafer, A. / Anzanello, F. / Yong, P. / Peng, L. / Dueker, K. / Musharrafieh, R. / ...著者: Zhou, P. / Song, G. / Liu, H. / Yuan, M. / He, W.T. / Beutler, N. / Zhu, X. / Tse, L.V. / Martinez, D.R. / Schafer, A. / Anzanello, F. / Yong, P. / Peng, L. / Dueker, K. / Musharrafieh, R. / Callaghan, S. / Capozzola, T. / Limbo, O. / Parren, M. / Garcia, E. / Rawlings, S.A. / Smith, D.M. / Nemazee, D. / Jardine, J.G. / Safonova, Y. / Briney, B. / Rogers, T.F. / Wilson, I.A. / Baric, R.S. / Gralinski, L.E. / Burton, D.R. / Andrabi, R.
履歴
登録2022年6月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年1月25日Provider: repository / タイプ: Initial release
改定 1.12023年3月1日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_DOI
改定 1.22023年3月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.32023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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 1.42024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

-
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

-
集合体

登録構造単位
H: Antibody CC95.108 Fab heavy chain
L: Antibody CC95.108 Fab light chain
A: Antibody CC95.108 Fab heavy chain
B: Antibody CC95.108 Fab light chain
C: Antibody CC95.108 Fab heavy chain
D: Antibody CC95.108 Fab light chain
E: Antibody CC95.108 Fab heavy chain
F: Antibody CC95.108 Fab light chain
G: Spike protein S2'
I: Spike protein S2'
J: Spike protein S2'
K: Spike protein S2'


分子量 (理論値)分子数
合計 (水以外)196,93512
ポリマ－196,93512
非ポリマー00
水00
1
H: Antibody CC95.108 Fab heavy chain
L: Antibody CC95.108 Fab light chain
G: Spike protein S2'


分子量 (理論値)分子数
合計 (水以外)49,2343
ポリマ－49,2343
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-30 kcal/mol
Surface area19860 Å2
手法PISA
2
A: Antibody CC95.108 Fab heavy chain
B: Antibody CC95.108 Fab light chain
I: Spike protein S2'


分子量 (理論値)分子数
合計 (水以外)49,2343
ポリマ－49,2343
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-31 kcal/mol
Surface area19860 Å2
手法PISA
3
C: Antibody CC95.108 Fab heavy chain
D: Antibody CC95.108 Fab light chain
J: Spike protein S2'


分子量 (理論値)分子数
合計 (水以外)49,2343
ポリマ－49,2343
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-33 kcal/mol
Surface area20090 Å2
手法PISA
4
E: Antibody CC95.108 Fab heavy chain
F: Antibody CC95.108 Fab light chain
K: Spike protein S2'


分子量 (理論値)分子数
合計 (水以外)49,2343
ポリマ－49,2343
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area20110 Å2
手法PISA
単位格子
Length a, b, c (Å)157.422, 157.422, 205.095
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 126 or (resid 127...
21(chain C and (resid 1 through 126 or (resid 127...
31(chain E and (resid 1 through 126 or (resid 127...
41(chain H and (resid 1 through 60 or (resid 61...
12(chain B and (resid 3 through 110 or (resid 111...
22(chain D and (resid 3 through 17 or (resid 18...
32(chain F and (resid 3 through 17 or (resid 18...
42(chain L and (resid 3 through 16 or (resid 17...
13(chain G and (resid 1226 through 1242 or (resid 1243...
23(chain I and ((resid 1226 and (name N or name...
33(chain J and ((resid 1226 and (name N or name...
43(chain K and ((resid 1226 and (name N or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNPROPRO(chain A and (resid 1 through 126 or (resid 127...AC1 - 1261 - 130
121SERSERSERSER(chain A and (resid 1 through 126 or (resid 127...AC127131
131GLNGLNLYSLYS(chain A and (resid 1 through 126 or (resid 127...AC1 - 2141 - 218
141GLNGLNLYSLYS(chain A and (resid 1 through 126 or (resid 127...AC1 - 2141 - 218
151GLNGLNLYSLYS(chain A and (resid 1 through 126 or (resid 127...AC1 - 2141 - 218
161GLNGLNLYSLYS(chain A and (resid 1 through 126 or (resid 127...AC1 - 2141 - 218
211GLNGLNPROPRO(chain C and (resid 1 through 126 or (resid 127...CE1 - 1261 - 130
221SERSERSERSER(chain C and (resid 1 through 126 or (resid 127...CE127131
231GLNGLNSERSER(chain C and (resid 1 through 126 or (resid 127...CE1 - 2151 - 219
241GLNGLNSERSER(chain C and (resid 1 through 126 or (resid 127...CE1 - 2151 - 219
251GLNGLNSERSER(chain C and (resid 1 through 126 or (resid 127...CE1 - 2151 - 219
261GLNGLNSERSER(chain C and (resid 1 through 126 or (resid 127...CE1 - 2151 - 219
311GLNGLNPROPRO(chain E and (resid 1 through 126 or (resid 127...EG1 - 1261 - 130
321SERSERALAALA(chain E and (resid 1 through 126 or (resid 127...EG127 - 137131 - 141
331GLNGLNLYSLYS(chain E and (resid 1 through 126 or (resid 127...EG1 - 2141 - 218
341GLNGLNLYSLYS(chain E and (resid 1 through 126 or (resid 127...EG1 - 2141 - 218
351GLNGLNLYSLYS(chain E and (resid 1 through 126 or (resid 127...EG1 - 2141 - 218
361GLNGLNLYSLYS(chain E and (resid 1 through 126 or (resid 127...EG1 - 2141 - 218
411GLNGLNALAALA(chain H and (resid 1 through 60 or (resid 61...HA1 - 601 - 61
421GLNGLNGLNGLN(chain H and (resid 1 through 60 or (resid 61...HA6162
431GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
441GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
451GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
461GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
471VALVALVALVAL(chain H and (resid 1 through 60 or (resid 61...HA142146
481LYSLYSLYSLYS(chain H and (resid 1 through 60 or (resid 61...HA143147
491GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
4101GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
4111GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
4121GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
4131GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
4141GLNGLNPROPRO(chain H and (resid 1 through 60 or (resid 61...HA1 - 2131 - 217
112VALVALPROPRO(chain B and (resid 3 through 110 or (resid 111...BD3 - 1103 - 113
122LYSLYSALAALA(chain B and (resid 3 through 110 or (resid 111...BD111 - 113114 - 116
132VALVALPROPRO(chain B and (resid 3 through 110 or (resid 111...BD3 - 2093 - 212
142VALVALPROPRO(chain B and (resid 3 through 110 or (resid 111...BD3 - 2093 - 212
152VALVALPROPRO(chain B and (resid 3 through 110 or (resid 111...BD3 - 2093 - 212
162VALVALPROPRO(chain B and (resid 3 through 110 or (resid 111...BD3 - 2093 - 212
212VALVALARGARG(chain D and (resid 3 through 17 or (resid 18...DF3 - 173 - 16
222LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DF1817
232VALVALPROPRO(chain D and (resid 3 through 17 or (resid 18...DF3 - 2093 - 212
242VALVALPROPRO(chain D and (resid 3 through 17 or (resid 18...DF3 - 2093 - 212
252VALVALPROPRO(chain D and (resid 3 through 17 or (resid 18...DF3 - 2093 - 212
262VALVALPROPRO(chain D and (resid 3 through 17 or (resid 18...DF3 - 2093 - 212
312VALVALARGARG(chain F and (resid 3 through 17 or (resid 18...FH3 - 173 - 16
322LYSLYSLYSLYS(chain F and (resid 3 through 17 or (resid 18...FH1817
332VALVALPROPRO(chain F and (resid 3 through 17 or (resid 18...FH3 - 2093 - 212
342VALVALPROPRO(chain F and (resid 3 through 17 or (resid 18...FH3 - 2093 - 212
352VALVALPROPRO(chain F and (resid 3 through 17 or (resid 18...FH3 - 2093 - 212
362VALVALPROPRO(chain F and (resid 3 through 17 or (resid 18...FH3 - 2093 - 212
412VALVALGLUGLU(chain L and (resid 3 through 16 or (resid 17...LB3 - 163 - 15
422ARGARGLYSLYS(chain L and (resid 3 through 16 or (resid 17...LB17 - 1816 - 17
432SERSERPROPRO(chain L and (resid 3 through 16 or (resid 17...LB2 - 2092 - 212
442SERSERPROPRO(chain L and (resid 3 through 16 or (resid 17...LB2 - 2092 - 212
452SERSERPROPRO(chain L and (resid 3 through 16 or (resid 17...LB2 - 2092 - 212
462SERSERPROPRO(chain L and (resid 3 through 16 or (resid 17...LB2 - 2092 - 212
113HISHISPHEPHE(chain G and (resid 1226 through 1242 or (resid 1243...GI1226 - 12421 - 17
123LYSLYSLYSLYS(chain G and (resid 1226 through 1242 or (resid 1243...GI124318
133HISHISGLNGLN(chain G and (resid 1226 through 1242 or (resid 1243...GI1226 - 12451 - 20
143HISHISGLNGLN(chain G and (resid 1226 through 1242 or (resid 1243...GI1226 - 12451 - 20
153HISHISGLNGLN(chain G and (resid 1226 through 1242 or (resid 1243...GI1226 - 12451 - 20
163HISHISGLNGLN(chain G and (resid 1226 through 1242 or (resid 1243...GI1226 - 12451 - 20
213HISHISHISHIS(chain I and ((resid 1226 and (name N or name...IJ12261
223HISHISGLNGLN(chain I and ((resid 1226 and (name N or name...IJ1226 - 12451 - 20
233HISHISGLNGLN(chain I and ((resid 1226 and (name N or name...IJ1226 - 12451 - 20
243HISHISGLNGLN(chain I and ((resid 1226 and (name N or name...IJ1226 - 12451 - 20
253HISHISGLNGLN(chain I and ((resid 1226 and (name N or name...IJ1226 - 12451 - 20
313HISHISHISHIS(chain J and ((resid 1226 and (name N or name...JK12261
323HISHISGLNGLN(chain J and ((resid 1226 and (name N or name...JK1226 - 12451 - 20
333HISHISGLNGLN(chain J and ((resid 1226 and (name N or name...JK1226 - 12451 - 20
343HISHISGLNGLN(chain J and ((resid 1226 and (name N or name...JK1226 - 12451 - 20
353HISHISGLNGLN(chain J and ((resid 1226 and (name N or name...JK1226 - 12451 - 20
413HISHISHISHIS(chain K and ((resid 1226 and (name N or name...KL12261
423HISHISGLNGLN(chain K and ((resid 1226 and (name N or name...KL1226 - 12451 - 20
433HISHISGLNGLN(chain K and ((resid 1226 and (name N or name...KL1226 - 12451 - 20
443HISHISGLNGLN(chain K and ((resid 1226 and (name N or name...KL1226 - 12451 - 20
453HISHISGLNGLN(chain K and ((resid 1226 and (name N or name...KL1226 - 12451 - 20

NCSアンサンブル:
ID
1
2
3

-
要素

#1: 抗体
Antibody CC95.108 Fab heavy chain


分子量: 23503.342 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#2: 抗体
Antibody CC95.108 Fab light chain


分子量: 22841.285 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: タンパク質・ペプチド
Spike protein S2'


分子量: 2889.177 Da / 分子数: 4 / Fragment: stem helix domain, residues 1226-1250 / 由来タイプ: 合成
由来: (合成) Human coronavirus HKU1 (isolate N1) (ウイルス)
参照: UniProt: Q5MQD0
Has protein modificationY

-
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: 2.48 Å3/Da / 溶媒含有率: 50.47 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M Ammonium formate, 20% (w/v) PEG 3350

-
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: SSRL / ビームライン: BL12-1 / 波長: 0.97946 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年11月22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: 0.97946 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 45677 / % possible obs: 99.1 % / 冗長度: 4 % / Biso Wilson estimate: 49.62 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.08 / Rrim(I) all: 0.164 / Χ2: 0.893 / Net I/σ(I): 7.1 / Num. measured all: 184320
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.51.13122310.3830.6781.3270.83797.9
2.85-2.93.61.05723030.4780.6141.2290.87398.2
2.9-2.964.20.80722580.6270.4450.9240.89799.9
2.96-3.024.20.76123110.6630.4190.8710.92499.9
3.02-3.084.20.61723010.7390.3410.7070.91399.9
3.08-3.154.20.49223310.8040.270.5630.91199.8
3.15-3.234.10.38423070.8750.2130.440.97100
3.23-3.324.20.32822730.9020.1810.3760.97199.8
3.32-3.424.10.26722780.9290.1480.3060.99499.5
3.42-3.534.10.2123180.9490.1170.2410.98299.5
3.53-3.654.10.16623160.9630.0930.1910.97199.4
3.65-3.840.14722520.9680.0830.1690.9699.4
3.8-3.9740.11222470.9810.0630.1290.93497.8
3.97-4.183.50.08822550.9820.0530.1030.88897.3
4.18-4.4440.07422980.9880.0420.0850.88499.4
4.44-4.794.30.06823030.9890.0370.0780.86399.9
4.79-5.274.30.06522920.9880.0360.0750.84799.7
5.27-6.034.20.06323100.9890.0350.0720.78799.8
6.03-7.5940.05722630.990.0320.0660.76598.3
7.59-503.90.04222300.9940.0230.0490.65796.7

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
HKL-2000データスケーリング
PDB_EXTRACT3.27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: 7JMW; 7KN4

7jmw

7kn4


解像度: 2.81→39.36 Å / SU ML: 0.33 / 交差検証法: THROUGHOUT / σ(F): 1.98 / 位相誤差: 26.28 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2481 2257 5.12 %
Rwork0.2167 41791 -
obs0.2183 44048 95.01 %
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: 134.64 Å2 / Biso mean: 51.3616 Å2 / Biso min: 18.82 Å2
精密化ステップサイクル: final / 解像度: 2.81→39.36 Å
タンパク質核酸リガンド溶媒全体
原子数13052 0 0 0 13052
残基数----1772
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2524X-RAY DIFFRACTION10.787TORSIONAL
12C2524X-RAY DIFFRACTION10.787TORSIONAL
13E2524X-RAY DIFFRACTION10.787TORSIONAL
14H2524X-RAY DIFFRACTION10.787TORSIONAL
21B2472X-RAY DIFFRACTION10.787TORSIONAL
22D2472X-RAY DIFFRACTION10.787TORSIONAL
23F2472X-RAY DIFFRACTION10.787TORSIONAL
24L2472X-RAY DIFFRACTION10.787TORSIONAL
31G228X-RAY DIFFRACTION10.787TORSIONAL
32I228X-RAY DIFFRACTION10.787TORSIONAL
33J228X-RAY DIFFRACTION10.787TORSIONAL
34K228X-RAY DIFFRACTION10.787TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.81-2.870.3839750.31771591166657
2.87-2.930.34951210.312189231079
2.93-3.010.33211860.30362626281297
3.01-3.090.3431660.31032670283698
3.09-3.180.33781270.28942742286999
3.18-3.280.29881260.263727922918100
3.28-3.40.2522980.25422735283399
3.4-3.530.30241370.2512769290699
3.54-3.70.28781720.24952690286299
3.7-3.890.30571470.2192709285699
3.89-4.130.23121360.19872699283598
4.13-4.450.20521420.1772725286799
4.45-4.90.19721370.162927572894100
4.9-5.610.18321840.172327092893100
5.61-7.060.19821780.20022690286899
7.06-39.360.1971250.1712698282397
精密化 TLS手法: refined / Origin x: -8.3909 Å / Origin y: 35.1759 Å / Origin z: -12.2123 Å
111213212223313233
T0.2124 Å2-0.0152 Å20.0412 Å2-0.1369 Å2-0.0488 Å2--0.3289 Å2
L0.2958 °20.0067 °2-0.0686 °2-0.1238 °2-0.22 °2--0.8435 °2
S-0.0166 Å °0.0555 Å °-0.0885 Å °-0.0115 Å °-0.0189 Å °-0.0609 Å °0.0224 Å °0.012 Å °0.0421 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 213
2X-RAY DIFFRACTION1allL2 - 209
3X-RAY DIFFRACTION1allA1 - 214
4X-RAY DIFFRACTION1allB3 - 209
5X-RAY DIFFRACTION1allC1 - 215
6X-RAY DIFFRACTION1allD3 - 209
7X-RAY DIFFRACTION1allE1 - 214
8X-RAY DIFFRACTION1allF3 - 209
9X-RAY DIFFRACTION1allG1226 - 1245
10X-RAY DIFFRACTION1allI1226 - 1245
11X-RAY DIFFRACTION1allJ1226 - 1245
12X-RAY DIFFRACTION1allK1226 - 1245

+
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

+
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。

-
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