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- PDB-7pqz: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

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基本情報

登録情報
データベース: PDB / ID: 7pqz
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A and FD-11A Fabs
要素
  • FD-11A Fab heavy chain
  • FD-11A Fab light chain
  • FI-3A Fab heavy chain
  • FI-3A Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 antibody / receptor-binding-domain / RBD / spike / neutralisation / FI-3A / FD-11A / FD-5D / 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 / 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 / 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 / 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
PHOSPHATE ION / Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 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
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 英国
引用ジャーナル: Theranostics / 年: 2022
タイトル: Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
著者: Kuan-Ying A Huang / Daming Zhou / Tiong Kit Tan / Charles Chen / Helen M E Duyvesteyn / Yuguang Zhao / Helen M Ginn / Ling Qin / Pramila Rijal / Lisa Schimanski / Robert Donat / Adam Harding ...著者: Kuan-Ying A Huang / Daming Zhou / Tiong Kit Tan / Charles Chen / Helen M E Duyvesteyn / Yuguang Zhao / Helen M Ginn / Ling Qin / Pramila Rijal / Lisa Schimanski / Robert Donat / Adam Harding / Javier Gilbert-Jaramillo / William James / Julia A Tree / Karen Buttigieg / Miles Carroll / Sue Charlton / Chia-En Lien / Meei-Yun Lin / Cheng-Pin Chen / Shu-Hsing Cheng / Xiaorui Chen / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Che Ma / Alain R Townsend / David I Stuart /
要旨: Administration of potent anti-receptor-binding domain (RBD) monoclonal antibodies has been shown to curtail viral shedding and reduce hospitalization in patients with SARS-CoV-2 infection. However, ... Administration of potent anti-receptor-binding domain (RBD) monoclonal antibodies has been shown to curtail viral shedding and reduce hospitalization in patients with SARS-CoV-2 infection. However, the structure-function analysis of potent human anti-RBD monoclonal antibodies and its links to the formulation of antibody cocktails remains largely elusive. Previously, we isolated a panel of neutralizing anti-RBD monoclonal antibodies from convalescent patients and showed their neutralization efficacy . Here, we elucidate the mechanism of action of antibodies and dissect antibodies at the epitope level, which leads to a formation of a potent antibody cocktail. We found that representative antibodies which target non-overlapping epitopes are effective against wild type virus and recently emerging variants of concern, whilst being encoded by antibody genes with few somatic mutations. Neutralization is associated with the inhibition of binding of viral RBD to ACE2 and possibly of the subsequent fusion process. Structural analysis of representative antibodies, by cryo-electron microscopy and crystallography, reveals that they have some unique aspects that are of potential value while sharing some features in common with previously reported neutralizing monoclonal antibodies. For instance, one has a common VH 3-53 public variable region yet is unusually resilient to mutation at residue 501 of the RBD. We evaluate the efficacy of an antibody cocktail consisting of two potent non-competing anti-RBD antibodies in a Syrian hamster model. We demonstrate that the cocktail prevents weight loss, reduces lung viral load and attenuates pulmonary inflammation in hamsters in both prophylactic and therapeutic settings. Although neutralization of one of these antibodies is abrogated by the mutations of variant B.1.351, it is also possible to produce a bi-valent cocktail of antibodies both of which are resilient to variants B.1.1.7, B.1.351 and B.1.617.2. These findings support the up-to-date and rational design of an anti-RBD antibody cocktail as a therapeutic candidate against COVID-19.
履歴
登録2021年9月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年2月2日Provider: repository / タイプ: Initial release
改定 1.12024年1月31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
E: Spike protein S1
H: FI-3A Fab heavy chain
L: FI-3A Fab light chain
A: FD-11A Fab heavy chain
B: FD-11A Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,7088
ポリマ－118,0945
非ポリマー6143
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-70 kcal/mol
Surface area46890 Å2
手法PISA
単位格子
Length a, b, c (Å)115.813, 115.813, 237.778
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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要素

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抗体 , 4種, 4分子 HLAB

#2: 抗体 FI-3A Fab heavy chain


分子量: 23521.436 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 FI-3A Fab light chain


分子量: 23364.842 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 FD-11A Fab heavy chain


分子量: 25032.070 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)
#5: 抗体 FD-11A Fab light chain


分子量: 23024.381 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 / 非ポリマー , 3種, 4分子 E

#1: タンパク質 Spike protein S1


分子量: 23150.891 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 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
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 2 / 由来タイプ: 合成 / 式: PO4

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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: 3.9 Å3/Da / 溶媒含有率: 68.45 %
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: 2.9 M sodium formate pH 7.0

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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: 0.97629 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年12月9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: 0.97629 Å / 相対比: 1
反射解像度: 3.2→100 Å / Num. obs: 31254 / % possible obs: 100 % / 冗長度: 98.9 % / Biso Wilson estimate: 145.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.027 / Net I/σ(I): 13.6
反射 シェル解像度: 3.2→3.26 Å / 冗長度: 103.3 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1532 / CC1/2: 0.381 / % possible all: 98.9

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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: 7PQY

7pqy


解像度: 3.2→76.66 Å / SU ML: 0.457 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.0473
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2401 1683 5.41 %
Rwork0.2006 29438 -
obs0.2028 31121 99.69 %
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: 167.1 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→76.66 Å
タンパク質核酸リガンド溶媒全体
原子数8045 0 38 0 8083
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00228277
X-RAY DIFFRACTIONf_angle_d0.510911270
X-RAY DIFFRACTIONf_chiral_restr0.04161256
X-RAY DIFFRACTIONf_plane_restr0.00461445
X-RAY DIFFRACTIONf_dihedral_angle_d10.96142937
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.40441200.38522357X-RAY DIFFRACTION96.53
3.3-3.40.37561520.33452430X-RAY DIFFRACTION100
3.4-3.520.30381560.30672376X-RAY DIFFRACTION99.96
3.52-3.660.28521330.26362418X-RAY DIFFRACTION100
3.66-3.830.27371420.25472447X-RAY DIFFRACTION100
3.83-4.030.25991430.22062422X-RAY DIFFRACTION100
4.03-4.290.24771330.21432444X-RAY DIFFRACTION100
4.29-4.620.23231600.1752437X-RAY DIFFRACTION100
4.62-5.080.21671450.18282455X-RAY DIFFRACTION100
5.08-5.820.29191200.18712503X-RAY DIFFRACTION100
5.82-7.330.26231260.20552516X-RAY DIFFRACTION100
7.33-76.660.18981530.16722633X-RAY DIFFRACTION99.71
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)
14.3061978404-2.89686261292-0.8766177740061.989841284030.847560696597.75991969765-0.0832569092106-0.0819343904130.6357744436211.216756404950.394003374198-0.7327064186660.391944311691-0.271393202427-0.01792131460531.29486111274-0.02698510094360.03356063944641.72777139459-0.1792314230331.7224954427-24.319241334315.5848551587-19.0458545245
21.78009166258-0.05446322780550.8225468667433.87301073682.458235138035.49900193783-0.5032227712980.7283985571580.5103895509170.532823263785-0.4342295817511.773314903261.01533834557-1.674572753910.3669452285961.62831526364-0.3352157370790.506393383211.82197128702-0.1807551910161.6538331297-32.6279631548.1015461315-25.4697884401
31.974428542221.34708352924-0.1863244564572.63741649977-2.095494865042.248611648850.1455808251910.3758649603-0.894840663007-1.60292743149-0.526274434354-0.2752064580110.637194628693-1.143314859880.2889853363241.57164989833-0.2772698159610.4386028394371.80812712355-0.2982019130041.8969952167-27.403923668711.3401858071-27.9622246181
40.6904109741181.269477553840.6819149046725.44726643495-2.673049231474.15380959223-0.1455000045920.504024962235-0.224407693812-0.4053701849860.05000776194230.8030349245490.3427136204880.2167308235040.04556554512261.06980755291-0.04465354177350.2279479135592.02211424281-0.408586695861.47490769227-32.002809287723.0169489696-31.7942043734
50.444953444493-0.822161811324-0.149047986465.03940266372-1.424987012222.06757063956-0.174952708020.166012218273-0.2465297801870.3101612285620.0463238127999-0.247223286220.0615830692759-0.1171424632380.4384946028651.02636702565-0.1836789510550.1570075674051.93092612838-0.1604795665341.43988971557-21.448499097935.887257312-27.004048404
65.137335758890.138706895652-1.988560633735.72793526274-2.528298064685.84617382351-0.6757837864050.232842660805-0.264843290981-0.7828677617090.8925725319682.18908744402-1.19040393751-0.379583153297-0.09053890415721.236328951420.03629111950910.2063553927851.64686102699-0.0970341730741.50852399103-36.523593396933.1003293946-17.0040058914
70.8063903940041.539496513960.01425716877054.70955198361-1.730633192191.36398920680.4521650549970.5290153546630.680970387727-0.878404323014-0.380923190199-2.049398136011.61312034936-0.9367217832540.2193491227021.62056964358-0.088428725830.5169383756481.91481056633-0.2268328949181.33683021155-27.611331133710.8776541357-26.7542599053
84.99069535616-4.248088692194.541522873624.08827675554-4.708512801295.53903540911-0.2811825265370.2648309025740.937141234468-0.518636820549-1.194148349580.6151308157780.1069459542150.5146478701521.21298750321.26399872975-0.04819951012040.1647460084662.15173387626-0.1350686929331.39387422555-37.198803353553.5049836563-50.814630962
98.43853398172-2.891259199977.258858934114.21720532086-1.968465390555.751915531820.1935566787240.624636872584-0.366357748611-0.391197920561-0.3766422936990.2493334706730.4040164678060.528596048786-0.05931387943451.042044758490.0807551688848-0.1262098326552.0555884982-0.2828652912871.10762818546-34.893836671944.6543814812-44.3116991691
105.73791820506-2.824089625815.523524710616.29746923531-3.305861627157.229136852680.2346915411641.168628475060.111779038534-0.701542125934-0.0310187695921.261685187670.2566143465381.62393561565-0.2491121680691.17629850126-0.03483592467370.07814422004972.46765677679-0.4630015905421.36461006274-43.346021125348.7139959596-46.8191858881
112.45333463527-0.9847111750192.740887580938.42930435955-0.6126748425198.74055754957-0.4460728933580.0342383261761.88117666878-0.06438436143330.128734040396-2.278282156510.6010586122780.4062525494070.2457417761081.02771141616-0.1369683553320.2735446448951.78980695691-0.387369652861.40084468725-30.512091174550.9108892772-33.4258642104
123.48322848069-4.39026352792-1.215166392894.277427582930.9479746610410.860080306388-0.2755173478070.5708347235510.550060352928-0.04872418598621.092807750110.3618358436480.255713537560.000793209678716-0.7882662013511.13115448809-0.0924215001324-0.156172716832.20121163803-0.1502057950741.52105398748-49.674600946671.414440887-53.2606392082
136.672155216560.281130064242.484010035022.927095382372.921727170334.09715692022-0.02280006719981.756656260960.0721671410227-0.1650964793650.94674273624-0.427506660973-0.2769577175230.823810489144-0.1444630610081.273081347250.131720319733-0.1898423558792.26105754096-0.009104362308791.69842250466-47.67083627973.4294565578-50.6503877279
141.659351852880.6827707679543.896207856339.067685729411.232740295956.036192937990.1941753097810.7224732686210.767563180369-0.339120912278-0.161952190415-0.4075708161410.1657242632660.5209498840920.06397174357791.1441755463-0.106388335274-0.07649200141321.98639947955-0.2594940175391.61308246243-45.748336290978.1269202155-47.7358145985
153.160952949112.184519732232.417408831051.554268555730.9766215884676.711966196870.3474379840831.57235570115-0.144764576589-0.633335130534-1.1708798727-0.409596815923-0.35873423261-0.1178156300470.09170487660581.23392441283-0.103484611320.04063960725212.118266002030.04041095338891.68600305972-44.364274096879.2542389763-57.2139112206
164.55305256381-1.50852735217-1.061835357465.250421109881.655426706745.1741618709-0.342225358601-0.498386856903-0.163848946840.574391300288-0.1225182489010.18355633906-0.03484692282870.1977738931360.5565792063880.9531429864840.0673881761813-0.004398349655911.84678557707-0.1128604368071.21698527223-42.17834925855.0230941617-23.2607563833
170.466513920995-2.58810439424-2.131352782029.262282378626.273724236915.0641489698-0.802606382820.63226022473-0.8812059778893.02240397173-0.6689911499392.753332359150.839716067497-0.8080648790581.070746545651.03597674576-0.137058540661-0.07186627425521.92188967776-0.2964045329751.46912495863-47.343352057158.7908504562-28.0271268524
184.65738687889-2.390950703544.821168458762.96825040639-0.5065256747156.961328420920.09079440880460.4150577095980.127703988385-0.236339391738-0.4383670741990.228065715208-0.2505950974420.01212959546470.3062460329711.00870921513-0.0297913576135-0.1157520983931.92574989903-0.139646772141.54367778483-61.023493639380.3424583692-44.2406540343
194.87984990632-1.02204101567-1.300809445472.85759072571-1.136395139357.54782711829-0.5229874193370.07800841183050.6386332657282.57436530547-0.0768240899581-0.002817480101951.118368200041.18296027142-0.3295895816981.537111928030.108741592524-0.446909160522.13161157305-0.1355293009981.65595036596-21.740799236226.530755932922.6616175307
205.563329542961.238253910590.1651193574958.28809503504-0.05126560976185.069327630620.00637427283806-0.2420957167520.133246681870.8672676312020.371154340995-1.29528815632-0.07892836405541.26187315981-0.3767154439641.491606133870.0837556460287-0.1604384310621.71185940503-0.2224239185231.50851377032-23.138284335830.830988521713.3153819665
216.370154573761.4401258629-3.448062082364.82339607504-0.4692015074139.56893124799-0.3299051469391.25193385411-1.062968371950.166766819660.314286584577-1.800575826420.3774155481110.566670016838-0.3265616050311.173738879140.2262143895730.07197533849831.58136603617-0.2243348047021.62119845085-27.389257036724.13825715270.623964532245
225.063810923690.936479160348-2.703922117612.6055238308-1.363779030421.995080114951.28643597675-0.0810233070256-1.096037827351.286567735640.649015356879-0.501404425725-1.09742891499-1.83086290211-0.55204918062.393483148280.071473614415-0.4695039268541.21312705324-0.165299938531.61111267267-28.140277347130.79987514735.7032378936
234.078147689641.048083331232.030049139046.815509791482.526901296967.068836291220.278447206273-0.1575591673930.5234512528751.700346624010.9070540313970.7681920480340.1765520633780.734954824144-1.110345310931.970047345350.400618715103-0.1724001694621.234903083-0.2237576772151.48331265469-47.601955114619.752743512951.4747344902
246.993680048952.80850066081-0.2968633735193.86518761269-1.899416922756.32377994888-0.823959122794-0.154412695465-0.4657117532480.3270303968731.04662586255-0.74006202831-0.5377397904360.173537915321-0.4648251181581.925150998440.359765525759-0.2164738627261.53149828488-0.2494584909131.39768103218-37.869961255820.624526541342.0444299819
253.588044140362.63480514193-2.808673260174.93965481015-6.686258902158.9297836008-0.462635707662-0.959741905486-0.00178896067816-0.6445039033770.02429540722290.02460971427160.88789986678-0.07255525453460.4670850609572.251786062420.275059433671-0.07694333887731.1966813608-0.1822487955551.49011679387-47.767652289110.926454289552.1164007602
265.99041908377-0.117090487303-0.6431627292194.3407435762.137145252968.88790906827-0.9701109911460.064716428361-1.18560684991.574177541260.597815895985-1.533654342160.9365682699340.836560847260.3916411035851.811243911380.281063489928-0.3338673669541.32709921609-0.1848150609441.52430940283-35.358739695718.016673751152.1129322631
274.681346219965.03058876239-4.873114054495.24011350684-5.232216057414.680039498420.48856112327-0.1135235017131.448546698722.025027094180.2961005360382.81411792119-0.350329556024-2.03606068378-1.170073761471.373797486710.1806399713860.2128723201791.724405525860.1526036111281.43668664838-50.762900698424.1000543369.47464892862
287.905777659065.44215911415-5.975930718228.11048880193-3.822265788737.783223673610.4428165461110.2269976804510.674892290492-0.506660249296-0.667853816938-0.269006032620.428020114258-0.2856749019680.2041450121031.336778132580.2506648056820.1264620447971.310992799910.04242187464261.28598779553-39.068383116625.39453974956.2345886193
297.203055974795.47293698641-4.329295635078.90252447825-6.632879147745.37968619466-0.2436165652250.382903744173-0.778362549803-2.24271328257-0.08034195072170.2696013613432.017057070980.535787579541.031439981421.76962297113-0.01108948950870.1637725829481.46204109049-0.00399660282271.66058486964-39.825589122514.75409658290.64873752632
306.89280683866.41814252396-3.135575408085.13496192834-2.446889017585.730464669560.02878157923160.3611226615920.162731134880.2296712263840.476978892423-0.359709861671-0.39126162433-0.645024189882-0.4169126447921.436779759520.2748956630330.03705732348381.38509101877-0.002348262017381.49517311878-42.097539497825.54930230666.28117788416
315.772637003553.43970606405-2.318667855074.99799171939-6.082497445018.594173150521.532475261540.7121600111251.256693805490.3979548250891.58460835575-1.090779076761.18194972779-1.57685067219-1.894966391221.483358973190.1835598337860.1271996514071.22723953971-0.1191181188321.85741815759-55.61099349715.167205420222.9311787854
325.384691776181.60020436149-0.114961529226.087103885222.541652831115.59595796423-0.414884092317-1.039668354380.3030794019410.6263369321210.123482149129-0.353637566135-0.228594356929-0.5303563023080.3732497663061.706289878640.561309165154-0.3060564930651.09676152977-0.04111681510681.37014167131-51.19662317925.859492595143.619947123
334.539616717494.363191605562.030846453344.011005037391.503479791969.03313451102-0.2457795936480.1473809537-0.09352346830170.6911014238460.643178133126-1.33335686782-0.3545380353210.251810575726-0.5452930640811.82666551180.2896367479-0.1419267408131.148875351850.02298231361511.45902073426-50.737749797325.99770797136.6211160017
349.090531984682.482080317373.861925761165.021109034022.731458846232.62072635392-0.373579951532-1.552911161550.2589332683090.7745508839410.5592973587030.3214695158260.376888885154-0.0970385076556-0.3322284122732.373346948960.525081635665-0.1217395631961.56947589931-0.1693903258721.62109876157-55.982657599333.870473108249.2615603271
354.115655045752.903378288333.732032661988.510217772955.568099029114.595565867910.778767069031-0.6305661959270.0306072616662-1.350313048921.58772474461-0.142241167666-3.28240584069-0.99633504299-1.370008507822.146934425670.365420779229-0.08805998014291.51029103772-0.1103122612271.66937978517-60.828211553424.788648750241.4493102657
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 'E' and (resid 334 through 353 )EA334 - 3531 - 20
22chain 'E' and (resid 354 through 387 )EA354 - 38721 - 54
33chain 'E' and (resid 388 through 403 )EA388 - 40355 - 70
44chain 'E' and (resid 404 through 437 )EA404 - 43771 - 104
55chain 'E' and (resid 438 through 494 )EA438 - 494105 - 161
66chain 'E' and (resid 495 through 506 )EA495 - 506162 - 173
77chain 'E' and (resid 507 through 526 )EA507 - 526174 - 189
88chain 'H' and (resid 1 through 17 )HD1 - 171 - 17
99chain 'H' and (resid 18 through 82 )HD18 - 8218 - 82
1010chain 'H' and (resid 83 through 97 )HD83 - 9783 - 97
1111chain 'H' and (resid 98 through 110 )HD98 - 11098 - 110
1212chain 'H' and (resid 111 through 138 )HD111 - 138111 - 135
1313chain 'H' and (resid 139 through 158 )HD139 - 158136 - 155
1414chain 'H' and (resid 159 through 204 )HD159 - 204156 - 201
1515chain 'H' and (resid 205 through 220 )HD205 - 220202 - 217
1616chain 'L' and (resid 1 through 90 )LE1 - 901 - 90
1717chain 'L' and (resid 91 through 113 )LE91 - 11391 - 113
1818chain 'L' and (resid 114 through 213 )LE114 - 213114 - 213
1919chain 'A' and (resid 1 through 17 )AF1 - 171 - 17
2020chain 'A' and (resid 18 through 98 )AF18 - 9818 - 98
2121chain 'A' and (resid 99 through 120 )AF99 - 12099 - 120
2222chain 'A' and (resid 121 through 133 )AF121 - 133121 - 133
2323chain 'A' and (resid 134 through 157 )AF134 - 157134 - 153
2424chain 'A' and (resid 158 through 191 )AF158 - 191154 - 187
2525chain 'A' and (resid 192 through 207 )AF192 - 207188 - 203
2626chain 'A' and (resid 208 through 229 )AF208 - 229204 - 225
2727chain 'B' and (resid 2 through 23 )BG2 - 231 - 22
2828chain 'B' and (resid 24 through 50 )BG24 - 5023 - 49
2929chain 'B' and (resid 51 through 63 )BG51 - 6350 - 62
3030chain 'B' and (resid 64 through 108 )BG64 - 10863 - 107
3131chain 'B' and (resid 109 through 120 )BG109 - 120108 - 119
3232chain 'B' and (resid 121 through 157 )BG121 - 157120 - 156
3333chain 'B' and (resid 158 through 187 )BG158 - 187157 - 186
3434chain 'B' and (resid 188 through 203 )BG188 - 203187 - 202
3535chain 'B' and (resid 204 through 216 )BG204 - 216203 - 215

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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://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る