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- PDB-7lop: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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基本情報

登録情報
データベース: PDB / ID: 7lop
タイトルCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV05-163 and CR3022
要素
  • (CV05-163 Fab ...) x 2
  • CR3022 Fab heavy chain
  • CR3022 Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM (ウイルス性) / SARS-CoV-2 (SARSコロナウイルス2) / receptor binding domain (受容体) / coronavirus (オルトコロナウイルス亜科) / COVID-19 (新型コロナウイルス感染症 (2019年)) / antibody (抗体) / Fab / IMMUNE SYSTEM (免疫系) / VIRAL PROTEIN-IMMUNE SYSTEM complex (ウイルス性)
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / 生体膜 / identical protein binding / 細胞膜
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
スパイクタンパク質
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.246 Å
データ登録者Yuan, M. / Zhu, X. / Wilson, I.A.
資金援助 米国, 5件
組織認可番号国
Bill & Melinda Gates FoundationOPP1170236 米国
Bill & Melinda Gates FoundationINV-004923 INV 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI139445 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI132317 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI142945 米国
引用ジャーナル: Science / 年: 2021
タイトル: Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants.
著者: Yuan, M. / Huang, D. / Lee, C.D. / Wu, N.C. / Jackson, A.M. / Zhu, X. / Liu, H. / Peng, L. / van Gils, M.J. / Sanders, R.W. / Burton, D.R. / Reincke, S.M. / Pruss, H. / Kreye, J. / Nemazee, D. ...著者: Yuan, M. / Huang, D. / Lee, C.D. / Wu, N.C. / Jackson, A.M. / Zhu, X. / Liu, H. / Peng, L. / van Gils, M.J. / Sanders, R.W. / Burton, D.R. / Reincke, S.M. / Pruss, H. / Kreye, J. / Nemazee, D. / Ward, A.B. / Wilson, I.A.
履歴
登録2021年2月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年3月3日Provider: repository / タイプ: Initial release
改定 1.12021年3月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22021年5月26日Group: Database references / カテゴリ: citation
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.32021年6月2日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.42021年8月25日Group: Database references / カテゴリ: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.52023年10月18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
W: CR3022 Fab heavy chain
V: CR3022 Fab light chain
B: CR3022 Fab heavy chain
C: CR3022 Fab light chain
Z: Spike protein S1
X: CV05-163 Fab heavy chain
Y: CV05-163 Fab light chain
H: CV05-163 Fab heavy chain
L: CV05-163 Fab light chain
A: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,79512
ポリマ－243,35210
非ポリマー4422
水22,2851237
1
W: CR3022 Fab heavy chain
V: CR3022 Fab light chain
Z: Spike protein S1
X: CV05-163 Fab heavy chain
Y: CV05-163 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,8976
ポリマ－121,6765
非ポリマー2211
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: CR3022 Fab heavy chain
C: CR3022 Fab light chain
H: CV05-163 Fab heavy chain
L: CV05-163 Fab light chain
A: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,8976
ポリマ－121,6765
非ポリマー2211
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)85.995, 132.884, 111.326
Angle α, β, γ (deg.)90.000, 100.680, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 334 through 465 or resid 467 through 528))
21(chain Z and (resid 334 through 465 or resid 467 through 528))
12(chain B and (resid 1 through 127 or resid 135...
22chain W
13(chain C and resid 1 through 214)
23chain V
14chain H
24chain X
15chain L
25(chain Y and resid 1 through 211)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 334 through 465 or resid 467 through 528))A334 - 465
121(chain A and (resid 334 through 465 or resid 467 through 528))A467 - 528
211(chain Z and (resid 334 through 465 or resid 467 through 528))Z334 - 465
221(chain Z and (resid 334 through 465 or resid 467 through 528))Z467 - 528
112(chain B and (resid 1 through 127 or resid 135...B1 - 127
122(chain B and (resid 1 through 127 or resid 135...B135 - 215
132(chain B and (resid 1 through 127 or resid 135...B216
142(chain B and (resid 1 through 127 or resid 135...B1 - 216
152(chain B and (resid 1 through 127 or resid 135...B1 - 216
162(chain B and (resid 1 through 127 or resid 135...B1 - 216
172(chain B and (resid 1 through 127 or resid 135...B1 - 216
182(chain B and (resid 1 through 127 or resid 135...B1 - 216
212chain WW1 - 216
113(chain C and resid 1 through 214)C1 - 214
213chain VV1 - 214
114chain HH1 - 216
214chain XX1 - 216
115chain LL1 - 211
215(chain Y and resid 1 through 211)Y1 - 211

NCSアンサンブル:
ID
1
2
3
4
5

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要素

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抗体 , 4種, 8分子 WBVCXHYL

#1: 抗体 CR3022 Fab heavy chain


分子量: 23455.420 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Mus musculus (ハツカネズミ)
#2: 抗体 CR3022 Fab light chain


分子量: 24376.963 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Mus musculus (ハツカネズミ)
#4: 抗体 CV05-163 Fab heavy chain


分子量: 24227.348 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Mus musculus (ハツカネズミ)
#5: 抗体 CV05-163 Fab light chain


分子量: 23521.076 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Mus musculus (ハツカネズミ)

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タンパク質 / 糖 / 非ポリマー , 3種, 1241分子 ZA

#3: タンパク質 Spike protein S1


分子量: 26095.348 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
遺伝子: S, 2 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P0DTC2
#6: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 1237 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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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: 2.57 Å3/Da / 溶媒含有率: 52.11 %
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 / pH: 4.8
詳細: 0.1 M sodium citrate - citric acid buffer at pH 4.8 and 19% (w/v) polyethylene glycol 6000

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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: APS / ビームライン: 23-ID-B / 波長: 1.0337 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年8月1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: 1.0337 Å / 相対比: 1
反射解像度: 2.246→50 Å / Num. obs: 115448 / % possible obs: 98.9 % / 冗長度: 3.2 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.094 / Rrim(I) all: 0.174 / Χ2: 0.858 / Net I/σ(I): 4.3
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
2.25-2.292.40.63853240.6150.4660.7950.50991.5
2.29-2.332.60.60255560.6730.4240.7390.47895.6
2.33-2.382.90.59156740.7080.4010.7180.4997.8
2.38-2.423.10.55657670.7430.3680.6690.45999.3
2.42-2.483.20.50558220.7750.3310.6060.48999.7
2.48-2.533.20.46257820.810.3040.5550.49699.8
2.53-2.63.10.38258590.8380.2590.4640.51499.9
2.6-2.673.30.36157930.8670.2360.4330.55499.9
2.67-2.753.30.31657790.8930.2080.3790.581100
2.75-2.833.60.28458490.9160.1740.3350.59999.9
2.83-2.943.70.24658200.9480.150.290.639100
2.94-3.053.60.21158090.9520.130.2490.71999.9
3.05-3.193.50.17458440.9620.1090.2060.831100
3.19-3.363.50.14958090.9710.0940.1760.98499.9
3.36-3.573.30.12258340.9760.080.1461.16499.7
3.57-3.853.10.10157890.9810.0680.1221.399.1
3.85-4.233.30.08257680.9890.0540.0991.33598.6
4.23-4.853.50.06857630.9910.0430.0811.54198.5
4.85-6.13.50.06758680.9920.0420.0791.32299.5
6.1-503.30.0659390.9950.0380.0711.68699.7

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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
PHENIX1.16_3549精密化
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: 6W41

6w41


解像度: 2.246→49.386 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 29.24 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.268 5783 5.01 %
Rwork0.2197 109607 -
obs0.2222 115390 98.65 %
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: 144.53 Å2 / Biso mean: 38.1268 Å2 / Biso min: 12.04 Å2
精密化ステップサイクル: final / 解像度: 2.246→49.386 Å
タンパク質核酸リガンド溶媒全体
原子数16407 0 28 1237 17672
Biso mean--49.2 37.22 -
残基数----2145
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1174X-RAY DIFFRACTION4.442TORSIONAL
12Z1174X-RAY DIFFRACTION4.442TORSIONAL
21B1282X-RAY DIFFRACTION4.442TORSIONAL
22W1282X-RAY DIFFRACTION4.442TORSIONAL
31C1326X-RAY DIFFRACTION4.442TORSIONAL
32V1326X-RAY DIFFRACTION4.442TORSIONAL
41H1370X-RAY DIFFRACTION4.442TORSIONAL
42X1370X-RAY DIFFRACTION4.442TORSIONAL
51L1284X-RAY DIFFRACTION4.442TORSIONAL
52Y1284X-RAY DIFFRACTION4.442TORSIONAL
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 (%)
2.2461-2.27170.36811400.3202312383
2.2717-2.29840.35681760.2915342294
2.2984-2.32640.34351960.2921356896
2.3264-2.35590.35151900.2769356197
2.3559-2.38690.32581830.272366699
2.3869-2.41960.30722090.2805365599
2.4196-2.45410.35981830.27253687100
2.4541-2.49080.34342050.26263640100
2.4908-2.52970.29421790.24863741100
2.5297-2.57110.30131760.24433669100
2.5711-2.61550.30682260.2433670100
2.6155-2.6630.29681910.24913741100
2.663-2.71430.31692100.24743658100
2.7143-2.76970.31061710.24463731100
2.7697-2.82990.28662060.24253674100
2.8299-2.89570.31621890.23313679100
2.8957-2.96810.31961730.23713743100
2.9681-3.04830.28282090.23383655100
3.0483-3.1380.30351910.23343665100
3.138-3.23930.31312020.22753742100
3.2393-3.3550.25641910.2183695100
3.355-3.48930.26751970.20823698100
3.4893-3.64810.24041890.2027366399
3.6481-3.84040.25592040.1999368599
3.8404-4.08090.23621990.1941366899
4.0809-4.39580.21561980.1708366499
4.3958-4.83780.17962260.1599361198
4.8378-5.5370.21361910.1746370799
5.537-6.97290.23731930.20553749100
6.9729-49.3860.23461900.2253377799
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)
12.59760.5101-0.48451.177-0.19530.9249-0.0177-0.2505-0.54770.163-0.1999-0.49640.04110.18750.21480.28540.0211-0.04670.24080.06530.314520.09418.28328.852
21.6790.1796-0.15361.6199-0.13271.3564-0.30370.305-0.4376-0.59810.0851-0.540.36420.12220.18340.30020.02720.01950.2413-0.01220.275716.58519.60717.986
30.7408-0.1033-0.00881.4025-0.74343.042-0.19960.20640.0257-0.22310.19120.02720.4218-0.47350.11470.2040.02520.05880.22490.02790.253719.27112.91418.266
40.77390.33580.02361.2656-0.0920.5780.0627-0.2406-0.2107-0.0795-0.1054-0.51170.1078-0.01320.06260.25840.0217-0.02750.24640.04250.450924.6221.65722.735
50.6211-1.2203-0.00313.6991-0.79330.5297-0.0118-0.2599-0.1190.9768-0.3698-0.6312-0.3513-0.20310.10890.3044-0.1329-0.22740.40460.14380.686442.6243.09132.202
61.6723-0.48810.40253.5227-0.29182.6091-0.3453-0.32980.19960.4818-0.092-0.1532-0.47090.30920.25410.3121-0.0298-0.04220.40810.10090.716643.21845.21829.557
71.61941.32070.55482.45831.99921.9273-0.0216-0.13090.05881.012-0.5237-0.9165-0.32920.360.15620.5-0.1295-0.32810.54510.28010.896247.55940.67136.778
80.99050.725-0.42351.82510.19851.47620.04270.03050.3208-0.2604-0.0829-0.0569-0.107-0.03580.11430.20560.0045-0.04010.2084-0.01850.210312.87942.78311.634
91.9441-0.6866-0.6351.2085-0.85062.01690.0776-0.0814-0.2122-0.02110.03090.0877-0.0127-0.2611-0.09610.2348-0.0201-0.02770.27090.02660.20866.81132.16316.51
101.4829-0.14510.33411.3770.15032.0610.2206-0.0219-0.23390.00450.0813-0.1779-0.1222-0.0442-0.18960.21230.02760.00040.2089-0.03980.17433.34939.11318.386
111.1818-0.5607-0.02122.5344-0.00040.4907-0.0022-0.12280.30260.98790.0026-0.13650.4412-0.3052-0.05960.28420.0036-0.06270.2252-0.01160.240613.31741.720.695
120.8306-0.3430.44750.7673-0.15560.94950.2494-0.2074-0.21150.0788-0.4163-0.79910.16720.0247-0.15010.1902-0.0123-0.00370.23480.12820.476331.09942.73619.097
130.39950.3763-0.04340.7468-0.04650.6306-0.20040.081-0.3117-0.1669-0.2388-0.5550.14590.1163-0.6375-0.0051-0.09170.02770.3820.22580.923940.26251.17416.991
141.91180.4820.48350.68420.68410.6734-0.303-0.56-0.5916-0.3469-0.2636-0.8706-0.05560.39970.21460.35440.01090.06620.36390.07290.707745.97146.36311.323
152.62510.4816-0.63570.64040.59851.414-0.12950.0707-0.05330.0145-0.1142-0.65570.0610.09610.20270.2933-0.0282-0.02110.32170.17330.694545.18252.00317.979
160.7243-0.46010.34481.33170.52750.82140.09490.1105-0.1583-0.27980.0195-0.19480.01350.0031-0.1490.3768-0.0326-0.07110.24720.07390.325520.9-18.66618.297
170.89480.22540.08561.66330.20361.2261-0.04770.10180.2598-0.32430.0614-0.3728-0.07890.00410.01840.2648-0.017-0.04620.22080.00570.252220.617-19.20929.297
180.16430.089-0.45180.75670.38871.894-0.0076-0.02340.1099-0.08480.0016-0.2065-0.13320.0847-0.01230.3262-0.0338-0.03710.2410.02010.384124.611-17.38725.226
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200.4715-0.35840.36081.808-0.17041.77940.3721-0.1409-0.2422-0.299-0.30070.1882-0.007-0.2876-0.03020.2449-0.0218-0.0240.2555-0.02290.26619.874-40.4134.784
212.67931.4646-0.12863.2505-0.62572.20280.35920.334-0.1418-0.26430.14570.49320.46140.1508-0.26210.30690.0288-0.06860.25010.01380.292428.75-41.9684.939
222.26751.22871.35714.80971.08823.47320.15190.0045-0.1741-0.2985-0.1748-0.2759-0.2047-0.3618-0.06950.36260.01790.00070.31690.02630.392419.341-41.408-2.744
232.54191.47950.16581.2859-0.81151.97060.04850.52270.3109-1.00820.1008-0.389-0.34440.21040.10450.41690.04010.05760.5426-0.01530.266823.8-43.114-8.01
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250.4008-0.0202-0.05061.07280.23390.77430.12370.11420.0469-0.0478-0.0346-0.5512-0.00430.0024-0.03350.31120.0429-0.02940.31150.01020.449834.485-45.23713.943
262.30770.468-1.27572.34910.48933.13180.11150.0350.0946-0.24930.0043-0.60630.07370.437-0.080.30750.07470.02370.280.03570.541137.303-51.5315.411
270.5223-0.7688-0.7182.61521.54733.33750.0414-0.1398-0.04780.0808-0.07320.4360.2922-0.38690.08820.1578-0.00770.04060.2449-0.00940.2464-14.6276.8126.065
282.2853-0.8549-1.81068.78375.37025.75450.12510.07930.68970.2503-0.36240.53320.0189-0.17470.12980.27960.0561-0.0130.2784-0.0320.4046-17.36416.60924.081
291.35180.29860.21850.8979-0.11522.17710.0453-0.02730.2361-0.0141-0.02930.3061-0.4983-0.1089-0.05530.3170.03520.03280.2995-0.0460.2575-3.77618.93226.532
301.29981.6221-0.48182.91160.75912.9206-0.17180.0764-0.1748-0.24410.0616-0.07040.24140.27970.05380.2744-0.03290.01740.23950.02250.1794-4.0534.23515.626
311.16070.59980.9261.39-0.37092.1716-0.0358-0.01530.00960.0157-0.0377-0.1178-0.11470.10590.11010.17940.01310.01650.1905-0.00160.1727-6.8-0.32118.82
320.61180.2372-0.71474.25240.93581.38510.10470.1185-0.0154-0.63710.04240.0125-0.3026-0.18-0.1230.2629-0.0174-0.03080.2225-0.00460.1729-13.154-3.4114.455
332.73350.3663-1.24613.78242.11532.7949-0.14750.1213-0.17740.0903-0.0946-0.15090.0743-0.17030.32730.301-0.0202-0.02760.21350.02780.1641-12.005-15.8865.091
341.27010.84860.65772.7347-1.49772.01310.1143-0.0088-0.0006-0.2339-0.0434-0.00820.24890.0484-0.09090.2173-0.02790.00120.2404-0.03430.1319-7.4767.69322.684
351.9213-0.120.88712.25080.8020.8495-0.0115-0.1387-0.1334-0.11220.27050.6099-0.13940.22680.38240.2752-0.00910.06090.20580.0330.17-26.861-40.65614.361
360.8630.1745-0.58452.5950.17161.4459-0.0387-0.0844-0.12580.53660.05480.58480.1345-0.00170.00960.21670.0339-0.00550.221-0.0290.2296-24.194-29.84616.328
371.01350.66470.53131.725-0.86581.36170.03330.10930.0686-0.1730.09110.1721-0.0666-0.0532-0.08530.15330.00410.00680.18060.00440.2142-21.812-338.774
380.99470.4205-0.10811.6940.28150.9172-0.1561-0.09620.25870.09060.17040.2407-0.05670.0443-0.03050.26490.04-0.04750.21450.05020.2548-17.907-28.5917.005
390.962-0.39980.8152.2176-0.3821.94630.1439-0.2947-0.2387-0.01410.03360.35930.2158-0.1516-0.18580.2488-0.0069-0.060.33960.06560.3965-15.052-66.9521.637
400.87361.1124-0.64891.67480.16184.40750.1544-0.1926-0.93410.15290.19410.48950.7969-0.1561-0.14380.5121-0.0534-0.0760.32590.09920.7356-18.829-75.47422.83
411.7192-0.023-0.09742.16660.47692.20.14160.09040.0622-0.0128-0.0703-0.46340.37890.1879-0.08430.25270.0041-0.02520.2121-0.02970.31612.125-33.77318.252
422.3837-0.09510.67581.91830.33330.76270.0472-0.376-0.52290.24030.02120.27320.1343-0.0094-0.05850.2898-0.0092-0.04010.24770.03960.2186-9.15-33.45723.116
430.6338-0.46770.95662.3335-0.43091.5071-0.0318-0.03960.02670.58510.1438-0.2073-0.00060.2364-0.06090.3365-0.0537-0.07960.2656-0.01010.2563-1.69-26.65426.315
440.7343-0.05360.34141.47260.13440.76080.08230.0557-0.23480.2517-0.0372-0.12330.09870.131-0.06970.1059-0.0166-0.04270.1801-0.00640.2016-4.572-48.51319.669
450.75240.00751.06293.0612.23494.5806-0.0362-0.06950.1014-0.0961-0.1164-0.02050.00680.3430.17060.14440.0272-0.00630.1924-0.00850.35940.385-63.78216.225
461.8766-0.23510.04541.85570.86141.91910.057-0.11890.00070.39950.0565-0.11090.35940.0691-0.06960.1182-0.0136-0.0390.09770.01690.1931-1.984-60.43517.471
472.2875-0.57160.37942.72840.28052.39840.170.093-0.0425-0.6107-0.01340.220.00910.0518-0.16950.37590.1075-0.06060.2589-0.08110.35430.354-70.40910.486
482.12210.99672.04632.89351.41635.30070.2647-0.61870.1210.52-0.35230.19160.8164-0.3537-0.02860.36970.01440.00110.30160.00580.50290.526-78.75414.522
490.4148-0.3391-0.58952.0537-0.26622.1117-0.11640.2754-0.25050.22010.28780.33470.15470.1687-0.02270.240.0231-0.0180.2153-0.00540.27186.79342.02171.406
500.7463-0.28280.05750.96570.27980.2827-0.0359-0.0789-0.00080.25-0.12730.32280.018-0.01550.1430.4486-0.02880.03410.2845-0.0010.2096.45531.06668.004
510.9351-0.44230.90781.58520.42611.46280.0311-0.1005-0.09850.4672-0.0397-0.2434-0.01780.0151-0.01940.3988-0.0074-0.01370.2413-0.00520.241414.21534.19569.608
520.8987-0.609-0.22171.34190.23910.6777-0.17260.02240.04190.48430.091-0.04940.23010.01390.01090.2830.04390.08060.18140.0151-0.03938.87229.81262.162
530.9052-0.88130.60892.4075-1.15790.61950.0102-0.1586-0.07960.28940.19990.0831-0.9031-0.2605-0.00440.71010.0219-0.01850.3077-0.01560.234612.19466.6868.224
541.1488-1.05841.66267.7325-5.8026.1117-0.35390.05640.2236-0.07160.0486-0.0196-0.3848-0.35490.04530.67310.0151-0.09870.41120.08370.45458.74474.58451.296
550.76180.7260.08711.5033-0.45161.0214-0.0146-0.20020.1380.3587-0.0940.0039-0.8967-1.0968-0.0670.52640.1908-0.02020.57220.01060.22132.86563.56362.155
561.3990.3462-0.37392.0758-0.59581.3449-0.1842-0.22420.29650.17880.19980.2029-0.8616-0.6319-0.06880.57370.1544-0.10170.4130.02190.335.19867.69356.796
573.02770.00791.56771.50241.45532.2173-0.5756-0.19950.5807-0.54420.12480.1698-0.95220.14150.1010.76240.1987-0.00910.38780.00020.84114.02277.05360.759
582.2952-0.2486-0.03262.5792-0.03251.179-0.0801-0.04940.5832-0.1956-0.1643-0.23380.1571-0.04340.12610.2785-0.06610.01790.2251-0.04690.245615.45239.96242.688
590.69050.9326-0.33851.8772-1.20041.95980.1810.1973-0.66480.233-0.2875-0.11220.5220.8060.25090.39740.030.04940.4096-0.01140.284420.47127.91146.316
601.01631.3926-0.31582.24040.41572.18310.1065-0.00960.24160.43-0.00130.2898-0.3473-0.1223-0.1140.30910.00710.01580.2153-0.00110.19147.84834.71251.699
610.6812-0.29160.91281.2714-0.641.280.11020.0544-0.18820.05250.00470.1462-0.1055-0.095-0.10520.27790.0161-0.03490.2811-0.05470.22828.62327.96343.609
620.28510.52030.08161.00470.44161.07790.02430.0798-0.0307-0.1576-0.10670.0750.2398-0.0560.04560.30760.0095-0.02460.2968-0.01830.14728.28537.25846.265
630.3669-0.21920.52762.1573-0.50212.9602-0.21670.07230.04690.1745-0.0554-0.6325-0.12560.19420.08590.1911-0.0237-0.01830.2601-0.01510.226615.50641.74547.265
641.28910.1576-0.84271.9767-0.44340.904-0.04710.19950.21820.01230.0777-0.23-0.7295-0.19950.12270.8228-0.0707-0.09270.20640.10260.274715.90676.59956.456
653.82351.62883.90660.69531.6223.98390.04570.51750.08570.3171-0.0032-0.2810.15160.57240.06110.5114-0.0973-0.08920.22950.05280.358218.58765.07846.749
662.90680.4035-0.60330.62820.53311.64160.16310.11420.095-0.06690.0735-0.2691-0.69050.4054-0.0660.52240.0062-0.03340.19840.09990.248426.16366.6952.027
672.06981.26560.41963.44610.34911.46410.2616-0.04720.05330.4976-0.2178-0.047-0.19750.00940.01230.4772-0.0575-0.07970.34340.01740.294416.04265.93951.706
680.92960.53040.71122.67511.81631.9868-0.16950.2048-0.01760.1840.1909-0.43480.02680.66850.10720.5135-0.1437-0.020.39240.03050.33622.90272.49643.496
693.12910.49571.00083.54590.45392.43110.3857-0.2098-0.12220.4311-0.18380.41880.3863-0.2089-0.14790.368-0.02860.00670.29110.01590.2442.369-6.42754.786
704.14282.03091.03254.07530.68840.2706-0.0595-0.387-0.17470.11480.0460.51310.6033-0.6849-0.08840.4068-0.16860.12510.42390.06960.4853.169-15.62758.395
711.9538-0.7850.20890.64330.66791.709-0.00740.1434-0.31980.1374-0.08720.22730.1031-0.23930.05910.4058-0.0293-0.06380.2732-0.04460.38267.664-17.78845.244
722.7891-0.09360.80371.56960.80042.71370.16690.1061-0.07770.22860.0313-0.12650.32960.1755-0.15310.32440.0179-0.0540.2302-0.04390.285714.978-4.05250.183
730.5773-0.60480.20511.8798-0.54260.7436-0.16860.03420.36080.06820.1289-0.2397-0.0360.0096-0.09660.34690.019-0.10670.2532-0.02640.311113.4439.69354.665
740.94980.4842-0.08571.47320.46160.1778-0.1636-0.03990.03480.5450.2338-0.42750.11520.0815-0.06010.41980.0654-0.15320.2811-0.02420.342822.3599.76163.607
752.0519-0.54870.60294.06880.25662.3581-0.0501-0.2759-0.1645-0.0486-0.0972-0.27960.2581-0.08670.13390.3164-0.0439-0.08170.3332-0.01590.30989.182-6.48750.383
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN W AND RESID 1:32 )W1 - 32
2X-RAY DIFFRACTION2( CHAIN W AND RESID 33:59 )W33 - 59
3X-RAY DIFFRACTION3( CHAIN W AND RESID 60:75 )W60 - 75
4X-RAY DIFFRACTION4( CHAIN W AND RESID 76:119 )W76 - 119
5X-RAY DIFFRACTION5( CHAIN W AND RESID 120:165 )W120 - 165
6X-RAY DIFFRACTION6( CHAIN W AND RESID 166:193 )W166 - 193
7X-RAY DIFFRACTION7( CHAIN W AND RESID 194:216 )W194 - 216
8X-RAY DIFFRACTION8( CHAIN V AND RESID 1:25 )V1 - 25
9X-RAY DIFFRACTION9( CHAIN V AND RESID 26:48 )V26 - 48
10X-RAY DIFFRACTION10( CHAIN V AND RESID 49:75 )V49 - 75
11X-RAY DIFFRACTION11( CHAIN V AND RESID 76:90 )V76 - 90
12X-RAY DIFFRACTION12( CHAIN V AND RESID 91:128 )V91 - 128
13X-RAY DIFFRACTION13( CHAIN V AND RESID 129:150 )V129 - 150
14X-RAY DIFFRACTION14( CHAIN V AND RESID 151:163 )V151 - 163
15X-RAY DIFFRACTION15( CHAIN V AND RESID 164:214 )V164 - 214
16X-RAY DIFFRACTION16( CHAIN B AND RESID 1:17 )B1 - 17
17X-RAY DIFFRACTION17( CHAIN B AND RESID 18:52 )B18 - 52
18X-RAY DIFFRACTION18( CHAIN B AND RESID 53:119 )B53 - 119
19X-RAY DIFFRACTION19( CHAIN B AND RESID 120:145 )B120 - 145
20X-RAY DIFFRACTION20( CHAIN B AND RESID 146:165 )B146 - 165
21X-RAY DIFFRACTION21( CHAIN B AND RESID 166:188 )B166 - 188
22X-RAY DIFFRACTION22( CHAIN B AND RESID 189:203 )B189 - 203
23X-RAY DIFFRACTION23( CHAIN B AND RESID 204:216 )B204 - 216
24X-RAY DIFFRACTION24( CHAIN C AND RESID 1:90 )C1 - 90
25X-RAY DIFFRACTION25( CHAIN C AND RESID 91:163 )C91 - 163
26X-RAY DIFFRACTION26( CHAIN C AND RESID 164:215 )C164 - 215
27X-RAY DIFFRACTION27( CHAIN Z AND RESID 334:353 )Z334 - 353
28X-RAY DIFFRACTION28( CHAIN Z AND RESID 354:364 )Z354 - 364
29X-RAY DIFFRACTION29( CHAIN Z AND RESID 365:393 )Z365 - 393
30X-RAY DIFFRACTION30( CHAIN Z AND RESID 394:421 )Z394 - 421
31X-RAY DIFFRACTION31( CHAIN Z AND RESID 422:459 )Z422 - 459
32X-RAY DIFFRACTION32( CHAIN Z AND RESID 460:479 )Z460 - 479
33X-RAY DIFFRACTION33( CHAIN Z AND RESID 480:494 )Z480 - 494
34X-RAY DIFFRACTION34( CHAIN Z AND RESID 495:527 )Z495 - 527
35X-RAY DIFFRACTION35( CHAIN X AND RESID 1:17 )X1 - 17
36X-RAY DIFFRACTION36( CHAIN X AND RESID 18:39 )X18 - 39
37X-RAY DIFFRACTION37( CHAIN X AND RESID 40:96 )X40 - 96
38X-RAY DIFFRACTION38( CHAIN X AND RESID 97:111 )X97 - 111
39X-RAY DIFFRACTION39( CHAIN X AND RESID 112:203 )X112 - 203
40X-RAY DIFFRACTION40( CHAIN X AND RESID 204:216 )X204 - 216
41X-RAY DIFFRACTION41( CHAIN Y AND RESID 1:31 )Y1 - 31
42X-RAY DIFFRACTION42( CHAIN Y AND RESID 32:48 )Y32 - 48
43X-RAY DIFFRACTION43( CHAIN Y AND RESID 49:75 )Y49 - 75
44X-RAY DIFFRACTION44( CHAIN Y AND RESID 76:128 )Y76 - 128
45X-RAY DIFFRACTION45( CHAIN Y AND RESID 129:150 )Y129 - 150
46X-RAY DIFFRACTION46( CHAIN Y AND RESID 151:174 )Y151 - 174
47X-RAY DIFFRACTION47( CHAIN Y AND RESID 175:204 )Y175 - 204
48X-RAY DIFFRACTION48( CHAIN Y AND RESID 205:215 )Y205 - 215
49X-RAY DIFFRACTION49( CHAIN H AND RESID 1:17 )H1 - 17
50X-RAY DIFFRACTION50( CHAIN H AND RESID 18:39 )H18 - 39
51X-RAY DIFFRACTION51( CHAIN H AND RESID 40:96 )H40 - 96
52X-RAY DIFFRACTION52( CHAIN H AND RESID 97:111 )H97 - 111
53X-RAY DIFFRACTION53( CHAIN H AND RESID 112:124 )H112 - 124
54X-RAY DIFFRACTION54( CHAIN H AND RESID 125:145 )H125 - 145
55X-RAY DIFFRACTION55( CHAIN H AND RESID 146:157 )H146 - 157
56X-RAY DIFFRACTION56( CHAIN H AND RESID 158:203 )H158 - 203
57X-RAY DIFFRACTION57( CHAIN H AND RESID 204:216 )H204 - 216
58X-RAY DIFFRACTION58( CHAIN L AND RESID 1:18 )L1 - 18
59X-RAY DIFFRACTION59( CHAIN L AND RESID 19:31 )L19 - 31
60X-RAY DIFFRACTION60( CHAIN L AND RESID 32:48 )L32 - 48
61X-RAY DIFFRACTION61( CHAIN L AND RESID 49:75 )L49 - 75
62X-RAY DIFFRACTION62( CHAIN L AND RESID 76:91 )L76 - 91
63X-RAY DIFFRACTION63( CHAIN L AND RESID 92:113 )L92 - 113
64X-RAY DIFFRACTION64( CHAIN L AND RESID 114:128 )L114 - 128
65X-RAY DIFFRACTION65( CHAIN L AND RESID 129:150 )L129 - 150
66X-RAY DIFFRACTION66( CHAIN L AND RESID 151:163 )L151 - 163
67X-RAY DIFFRACTION67( CHAIN L AND RESID 164:188 )L164 - 188
68X-RAY DIFFRACTION68( CHAIN L AND RESID 189:211 )L189 - 211
69X-RAY DIFFRACTION69( CHAIN A AND RESID 333:353 )A333 - 353
70X-RAY DIFFRACTION70( CHAIN A AND RESID 354:364 )A354 - 364
71X-RAY DIFFRACTION71( CHAIN A AND RESID 365:393 )A365 - 393
72X-RAY DIFFRACTION72( CHAIN A AND RESID 394:442 )A394 - 442
73X-RAY DIFFRACTION73( CHAIN A AND RESID 443:459 )A443 - 459
74X-RAY DIFFRACTION74( CHAIN A AND RESID 460:494 )A460 - 494
75X-RAY DIFFRACTION75( CHAIN A AND RESID 495:527 )A495 - 527

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万見について

-
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

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