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- PDB-7q0h: Crystal structure of the receptor binding domain of SARS-CoV-2 be... -

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基本情報

登録情報
データベース: PDB / ID: 7q0h
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54
要素
  • Beta-50 Fab heavy chain
  • Beta-50 Fab light chain
  • Beta-54 Fab heavy chain
  • Beta-54 Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 alpha variant / beta variant / gamma variant / delta variant / B.1.1.7 / B.1.351 / P.1 / B.1.617.2 / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
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)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.65 Å
データ登録者Zhou, D. / Ren, J. / Stuart, D.I.
資金援助 英国, 2件
組織認可番号国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 英国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
引用ジャーナル: Cell Host Microbe / 年: 2022
タイトル: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
著者: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James ...著者: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James Brett Case / Yuguang Zhao / Donal T Skelly / Rita E Chen / Sile Ann Johnson / Thomas G Ritter / Chris Mason / Tariq Malik / Nigel Temperton / Neil G Paterson / Mark A Williams / David R Hall / Daniel K Clare / Andrew Howe / Philip J R Goulder / Elizabeth E Fry / Michael S Diamond / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape ...Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
履歴
登録2021年10月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年12月22日Provider: repository / タイプ: Initial release
改定 1.12021年12月29日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22022年1月26日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
H: Beta-54 Fab heavy chain
L: Beta-54 Fab light chain
B: Beta-50 Fab light chain
A: Beta-50 Fab heavy chain
E: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,9166
ポリマ－119,0215
非ポリマー8951
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-49 kcal/mol
Surface area46320 Å2
単位格子
Length a, b, c (Å)102.207, 42.472, 138.406
Angle α, β, γ (deg.)90.000, 99.935, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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抗体 , 4種, 4分子 HLBA

#1: 抗体 Beta-54 Fab heavy chain


分子量: 24547.523 Da / 分子数: 1 / 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 Beta-54 Fab light chain


分子量: 23264.871 Da / 分子数: 1 / 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: 抗体 Beta-50 Fab light chain


分子量: 23792.414 Da / 分子数: 1 / 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)
#4: 抗体 Beta-50 Fab heavy chain


分子量: 23769.736 Da / 分子数: 1 / 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)

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タンパク質 / 糖 , 2種, 2分子 E

#5: タンパク質 Spike protein S1


分子量: 23646.551 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#6: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 894.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

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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: 2.49 Å3/Da / 溶媒含有率: 50.53 %
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
詳細: 0.1 M Tris pH 8.0, 28% w/v Polyethylene glycol 4,000

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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: Diamond / ビームライン: I03 / 波長: 0.9762 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2021年9月29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: 0.9762 Å / 相対比: 1
反射解像度: 3.65→89 Å / Num. obs: 13577 / % possible obs: 100 % / 冗長度: 6.8 % / Biso Wilson estimate: 98.77 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.55 / Rpim(I) all: 0.226 / Net I/σ(I): 3.7
反射 シェル解像度: 3.65→3.71 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 655 / CC1/2: 0.434

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解析

ソフトウェア
名称バージョン分類
GDA1.19_4092データ収集
PHENIX1.19_4092精密化
xia2データ削減
xia2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: 7PS6

7ps6


解像度: 3.65→88.62 Å / SU ML: 0.6458 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 30.9104
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3028 705 5.2 %
Rwork0.2547 12841 -
obs0.2572 13546 99.73 %
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 mean: 125.67 Å2
精密化ステップサイクル: LAST / 解像度: 3.65→88.62 Å
タンパク質核酸リガンド溶媒全体
原子数8135 0 60 0 8195
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00298406
X-RAY DIFFRACTIONf_angle_d0.595311456
X-RAY DIFFRACTIONf_chiral_restr0.04391303
X-RAY DIFFRACTIONf_plane_restr0.00491460
X-RAY DIFFRACTIONf_dihedral_angle_d11.61863007
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.930.36441490.32612505X-RAY DIFFRACTION99.1
3.93-4.330.34241360.28722525X-RAY DIFFRACTION99.85
4.33-4.950.30081360.24312544X-RAY DIFFRACTION99.96
4.95-6.240.26871240.25832601X-RAY DIFFRACTION99.93
6.24-88.620.28241600.21912666X-RAY DIFFRACTION99.86
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)
15.0072747888-0.5187931053662.534421977023.542075684630.6150928693734.325574692690.675359752877-0.992562780004-0.8824819611370.360372155980.0692439620465-0.1229497807290.290111120429-0.00766609703812-0.5755047574630.588707068771-0.0460176190595-0.04400273079420.7613868839250.2320690855530.88092314409233.7120184921-9.0153469649126.8672106236
24.77834779905-0.5215582766572.496756603591.28782316134-1.062397339565.909910009190.155802248138-1.61791109252-0.1898234497920.6122232510710.171844803471-0.28899358243-0.3241546796820.778370010938-0.4647450267950.8170576642830.0515465643869-0.1994321094971.46620244823-0.2910502506650.81941961371954.4831553127-1.812265905736.8820195714
33.52579512548-1.540902246260.9775610759844.73199014617-0.1967025267453.146816593210.0111395551862-1.105110922470.185357671832-0.1803503040521.025636006650.85299365662-0.5081066879780.54456913775-0.8737196567540.717519585834-0.1891741565060.1665925215591.50978974836-0.01949703459060.92409472730860.02620881562.534362195342.4397084035
45.11259808141.850457719720.2091637391072.697272869221.103702099111.000768003180.2961288172141.78385590499-1.2044562431-0.4490944221780.000278768839129-0.197546319267-0.002688923061680.340926366966-0.2836558189370.7294986403430.0524430590831-0.1076154858231.40755506289-0.2919830907320.99595437712647.1244360767-1.95937516897.99660994608
56.08007350597-1.461731802073.81269796631.18624853194-2.320347497475.99121111936-1.625581398190.8263203122562.325747693210.484501159632-0.995934535555-0.781975341039-1.142461345810.5273814015891.602738164311.01028450403-0.306624169607-0.06336591544060.8385076324060.1057270178430.94499946885442.05103209517.0217348860815.7504351753
65.33206760169-0.6272217223611.346401890283.00476389246-1.447779408283.95215781043-0.4032945591361.741529585770.0464582673809-0.4002671969980.4627501935590.7568950823310.1241440634760.75636733231-0.060778392880.568838764176-0.05099590194560.02244856244560.74960083813-0.01052609228830.83929366687144.8363873910.42495971167910.61149218
71.30312572441-1.454054777813.498174935371.5891759904-3.829386102619.69922077975-0.4904633347880.52318951899-0.979019117658-0.214288740223-0.307581329743-0.683788432316-0.5232864848311.45125321803-0.04501257148120.6774628207110.0647970074467-0.1278545518411.57378660796-0.1908170567311.0251078781564.21445398116.6044870945317.2036513289
84.50577205119-2.673472789970.01418845410252.74238532277-2.534151210394.931406657750.864928294481-0.890089040658-0.5082530002050.4998691959050.8531020934031.55859178533-0.4130104747010.225419511087-0.1054674986870.8343881372-0.246975250721-0.04426709362541.86850103085-0.3951964062571.2414701322970.95114178520.47250349030337.9596391812
95.05115360203-2.729177136280.823309931264.745976196480.7183965489990.538498823021-0.157848905322-0.846629390823-0.610537339964-0.138377832902-0.583800189543-2.723762759190.2947336136391.93934175116-0.457954213899-1.580336888550.0346064325773-0.147388805693.11609043488-0.07695849393650.99937074348381.8410112882-5.4667534304433.3562372421
104.34134332152-0.417029502880.6467759224922.20556786797-0.7604870486233.213263600720.207166864676-0.342329818155-0.1376666983390.0702172638239-0.365012607839-0.8966665408350.5077024150722.51124498993-0.1477951642650.3879318056060.0560032101585-0.2588762374131.655924439210.1708771231741.414649682572.5917272601-2.3902774132234.5390427396
113.83096991223-1.096246663351.462176644234.95175932954-1.161802958190.6288309620291.334759641941.71273172790.152376420442-0.3036602919071.712958327351.180264372781.007156331581.06790335748-0.5956730723231.06552145043-0.41248621978-0.241263509752.67437581883-0.1628377820160.96993175261481.58324842944.3655023362336.1193176994
124.13591336494-0.3082881833611.269913952454.778273418361.759440368767.005746602160.898486807136-0.1925276434541.47109381318-0.4983257295530.209704878275-0.595495609145-0.6321371505350.0918490264862-0.8495849464940.9730777943310.07573285608420.1424722532750.634116001386-0.1147441206510.86966040557620.3254940892-36.104909929134.8110742392
134.10970338884-2.527926635260.03530230507863.264108559720.6713658088686.088891404460.8651999333380.505255243126-0.1551192394240.00741640368964-0.440337464987-0.988952751855-0.9681490293460.07124629731-0.02697039914530.721690805014-0.0398374342521-0.02539370627960.8935510093780.2077316539490.72982635330113.723465724-28.778916747731.106725829
149.083307990441.66886442249-0.4159251905324.546385466571.894235777744.57709299762-0.580062103457-0.4590998983182.755851676441.07017440753-0.311584743085-0.146506813337-0.9169029932711.25505460818-0.2655144243690.722201754991-0.258823805232-0.1091467284641.017261248220.07490143752461.4811731324721.3397942478-27.313031978538.1239167961
150.8552849534660.6945686981770.1823638220061.644706769480.3592310244010.4879477550590.01833878647161.82628853915-0.939661277736-1.80162676119-0.8246465682650.0855127542851.57538190690.6951294007370.182131400430.7675623296020.147861752528-0.05939344810441.14654605981-0.1098822049430.8213209068252.72701598647-34.352448950132.904110622
164.032226564480.0583986042759-1.663800350011.281938553181.022484831617.13037195753-1.5407371431-2.10323526120.7756876671712.05510710464-0.862151150468-0.2970002880311.930349165562.45695601939-0.5508191791051.402218092780.3681257215590.1518551413791.316362491930.1747721247451.1164045868631.5686314839-36.842799419545.7784819851
171.468236180732.427503820242.791926259584.268306380235.028657789775.88220739737-1.95955105367-1.6474204512-0.469018463937-0.525179511977-1.961152038990.129558791353.21551163005-0.3604639490871.37514456062.261884969561.042998337770.6891574870713.085621572340.4541645610021.7451584905722.9823899958-44.969332353573.364796453
184.89574162768-0.2160332268623.79198390413-0.0415866204668-0.2076770575653.093314377790.5977933378562.36857845644-1.824984453571.88621065233-0.121024574141.636394647331.743262487940.8969280406790.7548611568222.530700703590.2998685517830.4576351416670.998712370144-0.09623181185661.348804999925.1437895769-45.921646821658.255017224
196.70080087835-0.224297879111-0.1424105509096.77881261368-1.207290266436.96826906798-0.359072425154-0.733374003751-0.4378344085821.0132865844-0.0702032791376-1.461187104061.20080863483-0.5814562445370.2399642511271.32236752233-0.0419071516449-0.3900161741711.294182134010.1991461365451.2138637456423.6086262735-42.442887149656.6235054018
200.106546213501-0.7079341776720.5341141042133.7810105361-2.58063591171.67848328112-2.19795055041-0.816663236772-3.04765476859-1.37279300087-1.081012804971.211502194652.498589765720.9348266379361.482021622553.286930893330.4425684070750.682722958560.2764666855090.3938203536932.1124774665720.9764055958-52.825691440867.9834596996
213.041238968540.716988044344-1.180393532810.1690130754550.1381483273995.227626858430.42372917018-2.07372755162-0.4370379831840.511353813294-0.1270653756740.2181883968841.828478412220.06755500150820.7139274408733.423207473131.519934723951.571738253151.459440535560.08727621083451.3682481053731.6305003717-51.907991145761.5934277556
225.87030511123-3.039997784830.02202955173553.64889355284-0.4424744579427.585508259910.109148256826-0.743329228952-0.5837805497570.2007688766260.5171367172380.5014969565590.145824824335-1.083136039950.01221565586020.766530277678-0.07807846671440.1096057181960.916278084246-0.1303918650210.648672491142-5.77897965756-29.875482769343.720204746
233.336637181540.3605703805480.282778989181.295692247421.271228398616.1781998922-0.747772778079-1.76511667550.4610226522881.183511626810.716071522692-0.6440395403570.348140743618-0.105288915590.009340912057311.382519527030.3786174937890.05549704958221.301220700570.0323349262390.93189110707213.0998583505-31.38125307961.4845400898
244.093097929563.154928382285.39798909346.502632129856.596802506488.48070195478-0.0306355061077-1.665904298030.4836839235720.0600235774778-1.005013060430.626815800762.211089415990.755581789185-0.1462315400660.7749669886880.337786205806-0.03979813564930.854929860025-0.114293700251.03741451734-6.09025348281-24.896203396822.0768217433
257.459206413274.23105794894-2.428768778342.15233878751-1.129465782325.83944392849-1.110919980340.265314974074-1.284516665691.646268033350.397583263839-1.883038761780.8302461503521.42725831004-0.4471993003730.7655689489620.335909387136-0.3089522849490.819542188387-0.06374206438670.5297515533384.28468495713-22.119446523611.8129713419
263.44864900583-1.33020455993-1.875253827182.82038333094-1.77674947993.74770956181-0.313403153998-1.500182428880.8632956429620.5241046199850.2059992146471.953725623530.1233455231730.677734366072-0.3912451184891.081636450660.2117061624640.2080104321050.9973052436910.1615658732320.916960087473-10.7279901642-13.729328943618.6238223119
274.86045850656-0.5269778437140.8608967442184.592375889471.233398381464.272423165060.2174352948490.3683084372210.157208290602-0.02534872912090.0913041048020.2601402851760.4962868233670.568990863855-0.3460692478030.574106010004-0.069331912837-0.0558369450860.599838972366-0.006041943302980.6333673174715.14666619051-13.47646271455.55429606042
287.294440946481.43394981485-2.611436622914.75071771124-1.331887064693.98520644056-0.06202962609223.352149429860.273918359107-0.203838112834-0.511201826189-1.74255065726-0.730584188737-0.016918597632-1.173152071570.6709739347310.0487426327196-0.08195701661351.430198247950.2175265385431.1969783265720.0340793857-18.5419459063-9.68899386325
292.539763117913.12858893383-1.245684167015.910108001780.2530499517632.289198366370.909962801899-0.726630714218-0.932357706110.714146338498-0.9225395984160.275245402339-0.5836004409060.3361480370550.1491774231380.3660068461730.06257377534-0.2754990763480.5870776498910.1154832489480.9690253919198.56279759601-10.046159444612.7774003552
305.45685913817-3.12626745692-2.201328973027.212203987020.9991569305373.92565099589-1.458770580371.52668560454-0.4940314804340.910741876863-0.2072992636891.403504838261.64972863674-0.804897178959-0.1311427761550.77182305886-0.2067143019140.01768077468391.407471972760.6885204941921.72582360424-18.0231702349-24.908475980212.4791692561
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 111 )HA1 - 1111 - 111
22chain 'H' and (resid 112 through 147 )HA112 - 147112 - 147
33chain 'H' and (resid 148 through 229 )HA148 - 229148 - 229
44chain 'L' and (resid 1 through 38 )LB1 - 381 - 38
55chain 'L' and (resid 39 through 61 )LB39 - 6139 - 61
66chain 'L' and (resid 62 through 101 )LB62 - 10162 - 101
77chain 'L' and (resid 102 through 113 )LB102 - 113102 - 113
88chain 'L' and (resid 114 through 143 )LB114 - 143114 - 143
99chain 'L' and (resid 144 through 155 )LB144 - 155144 - 155
1010chain 'L' and (resid 156 through 198 )LB156 - 198156 - 198
1111chain 'L' and (resid 199 through 214 )LB199 - 214199 - 214
1212chain 'B' and (resid 1 through 18 )BC1 - 181 - 18
1313chain 'B' and (resid 19 through 76 )BC19 - 7619 - 76
1414chain 'B' and (resid 77 through 90 )BC77 - 9077 - 90
1515chain 'B' and (resid 91 through 105 )BC91 - 10591 - 105
1616chain 'B' and (resid 106 through 116 )BC106 - 116106 - 116
1717chain 'B' and (resid 117 through 131 )BC117 - 131117 - 131
1818chain 'B' and (resid 132 through 153 )BC132 - 153132 - 153
1919chain 'B' and (resid 154 through 177 )BC154 - 177154 - 177
2020chain 'B' and (resid 178 through 200 )BC178 - 200178 - 200
2121chain 'B' and (resid 201 through 216 )BC201 - 216201 - 216
2222chain 'A' and (resid 3 through 73 )AD3 - 731 - 71
2323chain 'A' and (resid 74 through 219 )AD74 - 21972 - 212
2424chain 'E' and (resid 332 through 342 )EE332 - 3421 - 11
2525chain 'E' and (resid 343 through 358 )EE343 - 35812 - 27
2626chain 'E' and (resid 359 through 393 )EE359 - 39328 - 62
2727chain 'E' and (resid 394 through 469 )EE394 - 46963 - 138
2828chain 'E' and (resid 470 through 494 )EE470 - 494139 - 163
2929chain 'E' and (resid 495 through 516 )EE495 - 516164 - 185
3030chain 'E' and (resid 517 through 527 )EE517 - 527186 - 196

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る