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- PDB-7zfc: SARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-3... -

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基本情報

登録情報
データベース: PDB / ID: 7zfc
タイトルSARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs
要素
  • Nanobody C1
  • Omi-18 heavy chain
  • Omi-18 light chain
  • Omi-31 heavy chain
  • Omi-31 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 / Beta / Omicron / BA.1 / BA.2 / RBD / antibody / Fab / Omi-18 / Omi-31 / VIRAL PROTEIN/IMMUNE SYSTEM
機能・相同性
機能・相同性情報


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / symbiont entry into host cell / 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 / 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)
Lama glama (ラマ)
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: 3.24 Å
データ登録者Zhou, D. / Huo, J. / 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 / 年: 2022
タイトル: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
著者: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...著者: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
履歴
登録2022年4月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年6月1日Provider: repository / タイプ: Initial release
改定 1.12022年6月15日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22022年6月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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11月20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: Omi-31 heavy chain
L: Omi-31 light chain
M: Nanobody C1
A: Omi-18 heavy chain
B: Omi-18 light chain
E: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)131,7167
ポリマ－131,3496
非ポリマー3671
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 area13620 Å2
ΔGint-50 kcal/mol
Surface area50970 Å2
単位格子
Length a, b, c (Å)105.000, 105.000, 234.476
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 , 5種, 5分子 HLMAB

#1: 抗体 Omi-31 heavy chain


分子量: 24802.873 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 Omi-31 light chain


分子量: 22780.051 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 Nanobody C1


分子量: 14659.114 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌)
#4: 抗体 Omi-18 heavy chain


分子量: 23376.338 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 Omi-18 light chain


分子量: 22833.049 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

#6: タンパク質 Spike protein S1 / SARS-CoV-2 Beta Spike protein


分子量: 22897.684 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
#7: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 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
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(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: 2.84 Å3/Da / 溶媒含有率: 56.7 %
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: 0.04 M Potassium phosphate monobasic, 16% w/v PEG 8000

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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: I04 / 波長: 0.9795 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年3月4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: 0.9795 Å / 相対比: 1
反射解像度: 3.24→85 Å / Num. obs: 24674 / % possible obs: 100 % / 冗長度: 14.1 % / Biso Wilson estimate: 125.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.073 / Net I/σ(I): 6.6
反射 シェル解像度: 3.24→3.29 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1231 / CC1/2: 0.298

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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: 7PS4

7ps4


解像度: 3.24→84.78 Å / SU ML: 0.6484 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 33.6053
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2987 1201 4.89 %
Rwork0.2442 23357 -
obs0.2469 24558 99.63 %
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: 146.06 Å2
精密化ステップサイクル: LAST / 解像度: 3.24→84.78 Å
タンパク質核酸リガンド溶媒全体
原子数8919 0 24 0 8943
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00219178
X-RAY DIFFRACTIONf_angle_d0.508312526
X-RAY DIFFRACTIONf_chiral_restr0.04241409
X-RAY DIFFRACTIONf_plane_restr0.00431613
X-RAY DIFFRACTIONf_dihedral_angle_d11.51863247
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.370.42521510.38012512X-RAY DIFFRACTION98.05
3.37-3.520.33961300.33952557X-RAY DIFFRACTION99.93
3.52-3.710.37121200.32832564X-RAY DIFFRACTION99.96
3.71-3.940.35351090.30932568X-RAY DIFFRACTION99.85
3.94-4.240.32971330.2662578X-RAY DIFFRACTION99.96
4.24-4.670.26141290.22632595X-RAY DIFFRACTION99.96
4.67-5.340.29251370.2212621X-RAY DIFFRACTION100
5.34-6.730.30561660.23972592X-RAY DIFFRACTION100
6.73-84.780.25171260.19882770X-RAY DIFFRACTION99.11
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)
18.98451809069-6.95002268127-6.352156013146.180487135186.492695157426.030333399741.399987457390.30740507711-0.273319325062-0.215611625188-0.7350389402770.412497407871-2.87897087688-0.457610924051-1.131663993151.10836563739-0.1269566341340.1155928043721.16481394760.2546658269981.4546115653226.38658690148.6107535739422.1275174457
23.304820260151.66047129466-0.2616154255653.71431669282.393275088784.42633959698-0.4219519007930.2099977281280.355481624701-0.1582796848810.6925592572310.398435992727-0.231197913190.777867067468-0.09975790623390.788099403953-0.172819781781-0.006928251337960.824891320649-0.1295674001571.108654368625.922140323-0.27684225331131.6130485166
30.5023752890761.293597954210.9504078902672.01388945925-3.068727917827.55156546809-0.266910818442-0.234102369864-0.08198988972780.332218054643-0.364116640665-0.6278495366790.1348424395691.63100850739-0.0546798376611.1261232988-0.1397051061840.05969956183951.126234212810.1008865368671.4701860226929.3622689217-1.0381474053430.9923971481
47.53299844497-1.10406806159-2.132290997453.97148906291.585259306314.7204508269-0.4372895365960.7358493628391.22244736841-1.13264178430.4064372221670.03693902805930.468819461806-0.6323256251330.4659907314130.928315661431-0.346300469366-0.2367049818151.020442681840.06082305321511.4043265659824.91666785313.8201462763116.782838721
55.08280734806-0.09664188006624.084866172266.589067439822.613369843734.28557554727-2.17446464672-1.05399842536-0.2567083547680.103737575949-0.2208079887561.89876374695-1.165978198011.639887177260.1489919809032.75405763337-1.3302338663-0.1449480547682.758530334510.7046901696473.0376463616713.08511716522.26833303991-16.2734508703
64.289577423524.096873736671.202195377758.79817735011-3.031526098353.89512975969-4.03925395281.08328432123.1089205282-1.088578708732.523457792473.82392667629-2.92831467014-0.671146064158-0.07158464559312.81113308183-0.456848241114-0.3232779892381.808630568710.4897705406751.4939713675117.48794042448.06164220825-4.25881952702
74.730827815215.904450768972.416909721489.997010092181.728366199059.23708265884-1.1623774365-2.54313689575-1.293851451-1.72530440630.5586429933210.20170851082-0.9361934992170.7739703413730.2829923207441.55461810194-0.267575230546-0.1823178599471.261458302640.3074465637131.4901702099318.82605877182.84482516258-1.58773902166
84.98600356826-3.69528789586-0.4355441618465.8078109052-2.009226151761.53791371703-0.1460009440990.0214098457462-0.0180584260962-1.26368422360.8519246796081.58136409243-0.0433766816466-2.62722881777-0.6956785456391.84642277137-0.247468942873-0.6440445483732.087998934370.6154671282121.9262491366213.107136789811.5636555388-9.26063773508
95.264720755931.478050054490.6103624222072.248388446383.130532954684.212247735470.07505289689920.635804358817-0.299740592159-0.320622734293-0.10488427363-0.04374319355830.7456427237420.205877599212-0.06100859965621.04739228846-0.0982569003662-0.04438770517460.9575570626440.05433047711751.1900113055816.4852083896-16.204987719925.1704482525
106.340993485352.170320329382.143694363656.54458074859-0.344714611035.74205767920.442210052081-0.534110293711-0.272946033399-0.27573537529-0.3725011557210.03301940290040.969803628816-0.0973619482628-0.0419582871031.06417316074-0.0340222144046-0.07741078368750.9508229705120.08620742874331.0257157502414.3306528454-14.268916526729.2250549409
110.1498205906930.2565236818490.9976088281842.03384193036-2.635340603757.9654996493-0.1526408047380.6936791817711.31132364287-1.31652680730.4619843709751.239474559421.02984665028-0.7632142667330.3828398114611.57863931787-0.328000494602-0.1443250377851.987969568180.1570389042491.212459865499.9833353388-13.16628694753.59700189772
127.652103197370.839327818542.966519001010.3764732321281.023014593292.89031568427-1.75309017812-0.04144068335892.20044931676-3.94292771260.1208116522040.5815853291751.79572747291.129480221191.214495261072.56570242541-0.8867014423410.2270907674022.352306434770.2146496204822.2223994353126.36100480385.28370658503-18.1572980992
131.62556830647-2.244442580530.01501621409083.02865098049-2.211304984259.82300124967-0.854478559476-0.341392623079-0.643802729293-3.928509912560.3755699472170.7922343615751.703704595411.73734895671.589097164521.96658026484-0.2621423587210.03526968348821.29302294820.421047427972.3514946099717.1320245476-9.86784072577-6.19317799911
143.38108244183-1.543373476831.261262609390.933589040987-0.6597566839570.507401573805-0.5672839967641.58299940896-0.0432159037187-0.8129782724451.60141498559-0.5263186790892.634567439820.691986615936-1.020729539692.692039510170.109661903320.595727956632.370135489690.2131863375221.8665113176827.8449528026-12.231236815-11.6655617334
153.377884578273.870126753532.164546396914.464603404060.3883101856528.2497676235-1.74225063990.6098586093660.581711898524-2.352643124471.098686251381.184981089761.47473635772-0.8968926192330.670672055031.87452654078-0.4006528923130.2169390273851.391135502990.1911779413371.1758150176319.8367334571-5.03120939487-6.73174218029
167.11723597539-6.665528869380.3261769875446.23766207317-0.3180059668070.02347324926262.27379343756-1.07440255003-1.79648087706-1.25255230488-1.164570123811.66800041430.620906886534-2.31687566840.8337753277582.16326778913-1.702453693020.5454363919373.23477587119-0.1476677259691.4095386837920.3146259035-12.7290696867-15.2126404435
172.08172994901-7.34250850778-0.6221749367736.63111303047-0.7393534655961.06129224942-0.5890411099870.809249926132-3.35216274556-1.842389704370.2395271958130.6832935985420.508692491899-0.0120821680044-0.3524147917733.30732957475-1.431393399-0.2915078842412.494217595710.3898405870711.2774837963115.6069464976-12.7390046989-14.6230269988
186.859519262140.413478920701-6.117267809513.5399050577-0.9010900308675.148870657410.833469775944-1.975277914080.050653946114-0.302764077916-0.447505465983-0.243989984326-0.6746661685612.5964501919-0.6261468922580.911411605402-0.0306409258327-0.1795758203451.83415635283-0.4515751951961.5568903091172.2901886887-6.4360312040164.8677714348
196.03892719323-5.763928224310.1913341027868.87352791477-5.261512934277.67183182378-2.93809328342-0.74468962206-0.7139997934922.112611064052.179606938152.30204702006-0.04826291234032.50802614068-1.014591996661.179791793710.1449086267090.04850026830542.19851136930.1123098125331.4224771139357.2366530948-14.923878826375.3425904477
208.873550638030.616960708092-0.4340626565356.82900179049-3.331202125164.89382557318-0.08240247183190.715051980287-0.6873214758290.4018009719260.0701733874423-1.13087990062-0.16053379968-0.523455497911-0.2788513137750.7332496500440.142006040441-0.07215015988741.27933933121-0.2808455993111.2794606422661.7285262748-10.516561122859.1945102223
213.871037088120.648850380453-1.547310796333.85865176992-0.2534130808412.238855178710.119556508864-0.0444669969418-0.4702133899690.5374008822720.272457538234-0.4901387955710.7032499160740.0995229767677-0.1938954977811.18545516537-0.0307424915304-0.2174594717931.71680703081-0.006213209771051.2710970265569.1750982695-15.590893264462.1179462066
228.041277515021.48992513336-0.6968672168776.94500397554-0.4978408849242.407384825911.226374596910.3042859048470.263572594094-0.371718814139-0.60139658435-0.847883719401-0.1850422558710.111676988356-0.1911706214920.8154466772420.149215936105-0.02921626167161.38413914991-0.1999508568631.3775005547869.6499931143-6.2156847072656.0442455452
235.64935918284-0.6898215436324.410023760872.63312183203-1.178533674432.630291378720.01803436642470.3746323007070.714426542597-0.3212764797180.5838378894441.18783741425-0.24147627099-0.227842044803-0.500345161160.9579505585970.04385973270910.02254615781531.49930140073-0.1380263687581.3083689795460.3154431512-5.9822992898361.9362468729
242.09328517615-0.495872786051.403511895195.10947079717-0.2435077732534.44788114487-0.0182566413196-0.665761786201-0.2337750204940.0353509633338-0.09103290114150.375542547037-0.156650343652-0.1700766262880.1976057552820.912583479483-0.123256136301-0.006338286708051.10877159512-0.1237809598520.95931931381136.59680719716.276050678867.9123612754
253.466208022453.205360162874.409941978694.150932799262.386819103797.003957920841.89058221749-1.34759678334-0.8398287843031.43018959959-2.0901303078-1.684142725460.00378196125739-0.1993799133410.5406253407381.194546747740.110025570872-0.06554406548041.01373722838-0.037540302161.2362331595258.143189128439.866826359471.348275107
261.378004533542.35800046289-1.728261141986.14498168527-3.759367501115.305993872480.338423472048-0.341762247947-0.4853729496820.285573442647-0.224680877593-0.7690697106230.271525075277-0.00284730039281-0.2266237636781.21152846586-0.122264625837-0.1930707658281.23995872540.01083173814291.2753603446959.434345205549.412692305168.2418608836
278.0040432154-2.872951432654.139785921172.2105945464-3.826546109656.86635564817-0.5237034552650.8731923004731.6119051283-1.354401885890.474019953898-0.169310339762-1.070558593370.355725768941-0.2964546210591.06980895731-0.26905559996-0.01426596359671.215647193870.2344440044981.2551945616444.421420437428.564755714342.0909642657
289.936328932662.644224436794.325019051866.41188270046-1.326586526184.02257416711.460813023032.23318787529-1.11785378273-1.58223617793-2.29436658496-2.017901866042.061603002251.46809045663-0.2587952899031.982074615610.3367141490530.2817957236650.7755872657460.004756086392411.3298067444644.657213518113.983520228843.2934992245
292.121991234753.42596741002-0.4276059957628.81806719886-1.459287587321.83801748449-0.442342557316-1.74854830735-0.0853546064324-0.969496512287-0.3316016809510.964808596599-0.8942460127131.384981054160.2834104097791.143109257470.0046532208413-0.1990552457591.152648064040.006349226235931.1416753981835.592971591123.479075806352.296369181
307.16217056730.930646848567-0.2221876021242.30026210338-2.26567604918.79747639531.053961909730.8980162670830.7612337149410.0382265358183-1.810520064522.368641836830.422842186666-0.4314575441910.2435747703941.43078592025-0.153647760320.1232402230871.46824570163-0.1066931126121.8334626387729.130405886619.248195582843.9435319052
312.013630887680.0510293820191-2.004431439018.940816550642.973400253177.58522347279-0.4612532697681.698480481021.54218564766-3.25015966459-0.0418520388931-1.773175609722.43971721328-0.6256631670270.2677690845511.98362493644-0.2118738757140.06261218185661.12787275734-0.1719434132570.92569317626639.922013197917.902068079140.1943319782
326.735512077891.166918278940.2150929437611.91033435695-2.427202638229.056290726540.2228930341240.3303232093421.90463661744-0.77009815571-0.05312355654151.1022438713-0.0305717023951-1.965291769870.1203417622111.45839344602-0.132371391776-0.05346517320220.970161515186-0.1113032818031.4925086911137.58783504827.641257847346.4122369535
333.2920013195-0.06903476344612.25084050517-0.0496440445862-0.244863769911.36215698805-0.4266381935751.52922387828-1.087654965911.189101849060.454223933051-0.863354253399-0.4250791299160.16604271048-0.09295088537691.23038519706-0.015505065852-0.05087745970631.186888348650.0921222021251.4436579232642.95661268611.460012291154.8940093269
345.154657387060.06791957173584.92934206460.5424175643020.9565571267215.83877059021-0.181281007832-2.041277821450.671047886299-1.578214825470.5353935942251.43528853874-0.3617466853011.446430597920.09487259009831.1384925348-0.358074876658-0.01608129578081.138235396050.1585369534871.3683725651747.265853497639.382705454644.0751945822
356.04654163381-0.02814846913993.047725555873.535643512581.462217302734.762435873940.254724249713-0.3490912025790.4607042043660.259342996761-0.5340582130370.1522394021510.4871795278890.254396191759-0.2002324956991.31745002097-0.107441153511-0.08375781933511.238620185950.1341803987651.4566905134564.050364113338.887053822259.7163903936
366.10590957795-0.4793962396361.43395333830.7025130821340.4103158466955.13637439656-0.0694697398463-1.63394562423-1.54345694421-0.6215002894870.7789973824920.5134238309750.765379747966-1.0682583192-0.2919311036741.80924997874-0.0986452301494-0.04218494222391.158942147040.09098461314331.280051381357.227335189135.444295870256.5576678448
378.51239320122-0.7757756989662.038127460011.853942318720.2185587532028.23022083631.103506402410.0492189074279-0.868503265457-0.244014821552-0.107910306154-0.07939116877070.8301489770630.573603966168-0.9781773028591.33094680230.0247805985471-0.121443931721.00318613213-0.07883294087211.3734779411767.941880692135.22978292456.9011625079
387.0867877695-6.08363861203-2.999472976036.085365097484.979320266535.27328197174-0.135199575833-0.517436537447-0.2833233000531.336162129140.5739482316651.771304663910.342100769228-0.4229213926460.1304707037810.819201470034-0.227961765131-0.1534056471811.17561182264-0.1178253690831.1073791347639.7454567049-26.760367990149.3900447947
399.87427661398-3.49330500075-4.08736686578.50813346170.1741967605335.98853976051-0.7444969009440.593341633427-0.346186249718-0.2912396681430.209472395882-0.3447537415071.268271436610.3291826816660.5048040633970.9816496613870.125259420317-0.1356961042371.03569326995-0.1765977084330.83472269212242.7269551884-23.576819841855.7162113837
409.029713185612.019871675432.888603137544.199443272012.715366011586.515405441550.5230070874390.458610382807-2.080805582271.42896307174-0.0842386900748-1.079480322361.017827710351.24561348975-0.4800669434531.031412853320.1996206397090.06225265061321.25001098580.2212498679521.5240639113748.0374665813-25.275290733264.6668061684
412.69155197789-1.535764898520.3590003664912.70758631761-1.776786927962.14905372134-0.340523607056-0.310686355727-0.2356396849310.2965646043370.130091397304-0.2488181653570.0130772134883-0.04297992106070.08025172893790.834523691197-0.0391971014824-0.1064659918991.13979179122-0.1381153977640.91840196357333.237851584-5.7472606587556.0988894999
425.28900462224-0.974204292239-2.031993447148.92948484012-7.235158608365.242294084330.1443552214120.804037057291-0.4222709023260.5104845412670.1834819389590.0596234831674-0.371675180644-0.324953326038-0.7393214964271.08191924114-0.2082768585440.01731458950491.01921330731-0.2369413805371.1770027564943.23874066-14.943744547155.1414393687
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 23 )HA1 - 231 - 23
22chain 'H' and (resid 24 through 61 )HA24 - 6124 - 61
33chain 'H' and (resid 62 through 112 )HA62 - 11262 - 112
44chain 'H' and (resid 113 through 134 )HA113 - 134113 - 134
55chain 'H' and (resid 135 through 149 )HA135 - 149135 - 149
66chain 'H' and (resid 150 through 172 )HA150 - 172150 - 172
77chain 'H' and (resid 173 through 192 )HA173 - 192173 - 192
88chain 'H' and (resid 193 through 228 )HA193 - 228193 - 228
99chain 'L' and (resid 1 through 49 )LB1 - 491 - 49
1010chain 'L' and (resid 50 through 101 )LB50 - 10150 - 101
1111chain 'L' and (resid 102 through 122 )LB102 - 122102 - 122
1212chain 'L' and (resid 123 through 133 )LB123 - 133123 - 133
1313chain 'L' and (resid 134 through 154 )LB134 - 154134 - 154
1414chain 'L' and (resid 155 through 165 )LB155 - 165155 - 165
1515chain 'L' and (resid 166 through 191 )LB166 - 191166 - 191
1616chain 'L' and (resid 192 through 201 )LB192 - 201192 - 201
1717chain 'L' and (resid 202 through 213 )LB202 - 213202 - 213
1818chain 'M' and (resid 1 through 24 )MC1 - 241 - 24
1919chain 'M' and (resid 25 through 32 )MC25 - 3225 - 32
2020chain 'M' and (resid 33 through 60 )MC33 - 6033 - 60
2121chain 'M' and (resid 61 through 83 )MC61 - 8361 - 83
2222chain 'M' and (resid 84 through 99 )MC84 - 9984 - 99
2323chain 'M' and (resid 100 through 124 )MC100 - 124100 - 124
2424chain 'A' and (resid 1 through 110 )AD1 - 1101 - 110
2525chain 'A' and (resid 111 through 138 )AD111 - 138111 - 134
2626chain 'A' and (resid 139 through 219 )AD139 - 219135 - 215
2727chain 'B' and (resid 4 through 17 )BE4 - 171 - 14
2828chain 'B' and (resid 18 through 31 )BE18 - 3115 - 28
2929chain 'B' and (resid 32 through 47 )BE32 - 4729 - 44
3030chain 'B' and (resid 48 through 60 )BE48 - 6045 - 57
3131chain 'B' and (resid 61 through 74 )BE61 - 7458 - 71
3232chain 'B' and (resid 75 through 89 )BE75 - 8972 - 86
3333chain 'B' and (resid 90 through 102 )BE90 - 10287 - 99
3434chain 'B' and (resid 103 through 114 )BE103 - 114100 - 111
3535chain 'B' and (resid 115 through 151 )BE115 - 151112 - 148
3636chain 'B' and (resid 152 through 172 )BE152 - 172149 - 169
3737chain 'B' and (resid 173 through 210 )BE173 - 210170 - 207
3838chain 'E' and (resid 331 through 349 )EF331 - 3491 - 19
3939chain 'E' and (resid 350 through 375 )EF350 - 37520 - 45
4040chain 'E' and (resid 376 through 394 )EF376 - 39446 - 64
4141chain 'E' and (resid 395 through 494 )EF395 - 49465 - 164
4242chain 'E' and (resid 495 through 523 )EF495 - 523165 - 193

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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