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- PDB-8qrg: SARS-CoV-2 delta RBD complexed with XBB-2 Fab and NbC1 -

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データを開く


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基本情報

登録情報
データベース: PDB / ID: 8qrg
タイトルSARS-CoV-2 delta RBD complexed with XBB-2 Fab and NbC1
要素
  • NbC1
  • Spike protein S1
  • XBB-2 heavy chain
  • XBB-2 light chain
キーワードVIRAL PROTEIN / Viral protein/immune system / SARS-CoV-2 / RBD / XBB-6 / Beta-49 / BA.2.86 / XBB.1.5
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 / viral translation / host extracellular space / 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 / viral translation / host extracellular space / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, 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Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Lama glama (ラマ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 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 Rep Med / 年: 2024
タイトル: A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
著者: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / ...著者: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / Thomas G Ritter / Megan Plowright / Thomas A H Newman / Lizzie Stafford / Barbara Kronsteiner / Nigel Temperton / Yuan Lui / Martin Fellermeyer / Philip Goulder / Paul Klenerman / Susanna J Dunachie / Michael I Barton / Mikhail A Kutuzov / Omer Dushek / / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible ...BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
履歴
登録2023年10月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年5月8日Provider: repository / タイプ: Initial release
改定 1.12024年5月22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_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年6月5日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.32024年11月6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
E: Spike protein S1
A: NbC1
H: XBB-2 heavy chain
L: XBB-2 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)85,45911
ポリマ－84,6854
非ポリマー7747
水3,369187
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 area9190 Å2
ΔGint-29 kcal/mol
Surface area32060 Å2
単位格子
Length a, b, c (Å)81.514, 104.647, 110.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

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抗体 , 3種, 3分子 AHL

#2: 抗体 NbC1


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)
#3: 抗体 XBB-2 heavy chain


分子量: 23750.648 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 XBB-2 light chain


分子量: 23339.766 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

#1: タンパク質 Spike protein S1


分子量: 22935.734 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
#5: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 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

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非ポリマー , 2種, 193分子

#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C3H8O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 187 / 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
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: 2.77 Å3/Da / 溶媒含有率: 55.6 %
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% (v/v) 1,4-Dioxane, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 3350

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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: 0.97628 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2023年8月8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: 0.97628 Å / 相対比: 1
反射解像度: 2.3→110 Å / Num. obs: 38675 / % possible obs: 91.1 % / 冗長度: 10.5 % / Biso Wilson estimate: 45.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rsym value: 0.026 / Net I/σ(I): 17.9
反射 シェル解像度: 2.3→2.34 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1109 / CC1/2: 0.743 / Rpim(I) all: 0.743

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解析

ソフトウェア
名称バージョン分類
GDA1.20.1_4487データ収集
PHENIX1.20.1_4487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 / 解像度: 2.3→48.69 Å / SU ML: 0.3038 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 25.2582
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2278 1846 4.78 %
Rwork0.1824 36754 -
obs0.1846 38600 90.98 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 57.8 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→48.69 Å
タンパク質核酸リガンド溶媒全体
原子数5744 0 50 187 5981
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00475934
X-RAY DIFFRACTIONf_angle_d0.68638060
X-RAY DIFFRACTIONf_chiral_restr0.0467881
X-RAY DIFFRACTIONf_plane_restr0.00591042
X-RAY DIFFRACTIONf_dihedral_angle_d12.18582127
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3418880.25341674X-RAY DIFFRACTION54.64
2.36-2.430.3196800.26082022X-RAY DIFFRACTION66.04
2.43-2.510.32081130.25582390X-RAY DIFFRACTION77.56
2.51-2.60.28381320.24912687X-RAY DIFFRACTION87.74
2.6-2.710.34241300.25482977X-RAY DIFFRACTION95.75
2.71-2.830.29221540.22353076X-RAY DIFFRACTION99.57
2.83-2.980.2711730.21133063X-RAY DIFFRACTION100
2.98-3.160.26161730.21353074X-RAY DIFFRACTION100
3.16-3.410.28411470.21133091X-RAY DIFFRACTION100
3.41-3.750.22041730.17543096X-RAY DIFFRACTION100
3.75-4.290.18721480.15263152X-RAY DIFFRACTION100
4.3-5.410.16021460.12993174X-RAY DIFFRACTION100
5.41-48.690.19871890.16543278X-RAY DIFFRACTION99.83
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)
10.347600790014-0.89857583414-0.873509110524.6024528776-0.09217525717657.697589844940.2157907339241.50680421311-0.0849785328438-1.80990420069-0.1192189272920.699610130198-0.122479101521-0.07045081187010.2567968609991.076895748030.251062701252-0.1329576160510.9285724434790.01595789839240.53206092837133.73182403882.90868497318-17.4921636782
24.207342939230.4600602841360.6216501203782.09555345396-0.1978666262851.280034906770.1863060048510.963384707603-0.415711273223-0.708568384323-0.0003121360836560.5083298884750.363429472295-0.0276470797201-0.08221033497480.6441431590010.0501044628633-0.1960591603650.539666065232-0.1084702661010.43574001822427.3180746761-2.11175337807-10.1337960469
32.72447778792-0.07953266619960.7159908572573.73460009305-0.1616562627473.472363414040.142525362330.326385185254-0.143392337673-0.49409661409-0.1371322567760.2171515004580.1130879168630.105779744433-0.0115357031620.3091414233070.0492271948691-0.05935200501310.2450988990050.006598683279320.23863531816135.88513385432.131188124370.695808017985
42.14842318433-0.409392787550.9468269049942.401034553841.042157334893.930536329520.02428947812150.2353882801120.159922157622-0.08354330327-0.124872959163-0.0521335316857-0.1448642583910.4056017294120.04770675354290.300671891976-0.001913386743880.02384822100310.2494262321760.0639539069320.26579439381941.80749939495.503357257674.85147249015
52.89536013736-0.4147091083192.197339740866.46793701591-0.7169969913841.66348224390.298955164618-0.29264708792-1.328673734160.127564071420.530284460901-0.4781587563140.2075971824590.495191979659-0.6210588333081.03619382966-0.134729180571-0.06651816937410.698351830760.001706660690371.3201799520727.9138750867-34.6396060488-3.05268677463
61.229202214-0.333035673734-1.170508668684.80227599396-0.9568872702184.788993390010.2574266113450.2765582969420.2659703779471.078318791920.789737713278-0.1261715036781.1505351068-0.583602064112-0.05912647129541.04780870159-0.181092896146-0.1348578384630.519627705929-0.1144638988730.91973766757922.9437375396-31.5597564934-4.53529659937
70.639541930821-0.146650813889-0.9201205839444.67859272657-0.4294323985644.42469513308-0.442934798747-0.3584952173380.7975190498311.251332181010.182287376147-1.562253995540.6070361735310.0122724717469-0.05448712810990.728446212595-0.0188334437932-0.1354810923740.4258080587640.05226388646411.3376883276127.7000384609-21.9806584776-1.89013330526
84.524821583250.978949629216-3.531475097125.195281977650.8865685611246.09353460084-1.348056869430.228349576373-0.397328694529-0.5077112854780.3352544467690.0451847983060.616921128375-0.6137834480520.867232461330.8981733183520.0513323155617-0.1756265722320.491125181018-0.2103344550871.1584556543327.1983812979-20.1850578595-9.56222188855
92.538977781380.6896497480921.50699855581.61927118551-1.042516222492.27426605752-0.2491935213070.595063705644-0.94927984576-0.3486466691950.133301465302-0.01256427865940.373550510743-0.04162261970920.1576223329650.794956030259-0.0609327596747-0.04859716409050.573739239423-0.2574095455250.99301846182325.2929619491-27.9184745348-11.6312698195
100.13055260338-0.2316375068070.4095123239796.985879482290.3096335960524.203452889780.618194890960.19690317513-0.890519368531-0.3954372845840.930431687212-0.4305785376470.1286547142771.30691717375-1.177617491880.9231249579820.0129131413307-0.1543066570920.920750798972-0.3997550814151.4719881416135.0064446928-30.9050421199-6.78358073673
115.09661759415-1.639735128830.2081963055864.111581614261.190467775061.49333621632-0.39173266741-0.663580140934-0.5696846053430.311626077640.06561884094960.4838619465040.364590832961-0.3336050044840.3964125331980.7388306198090.0258005127387-0.1289834578910.391546323584-0.004246981113390.79183531814228.6234886246-17.27404499780.345880924759
121.922992463671.18546736946-0.3976183731021.409931711290.008461660757981.1270131816-0.7830969478110.846732445431-0.546501508856-0.597052336164-0.399210923199-0.432955555070.225772364371-0.3306737324951.269665573651.20010666030.232223096952-0.4599020910480.837158201775-0.02949896841182.137675481537.4586507627-38.5667198862-4.31812593344
136.319989882283.99410802698-3.889998079295.88286255357-4.696061398388.333129279230.319103782663-0.6851784375270.05252394915210.636525353301-0.2538415326730.145494723577-0.5309316957810.0913240493766-0.04845241215620.2386300704630.08271854737640.04040166154610.3618311421580.01825746245950.26324499078135.642225061-3.8567741898836.4191276778
141.875237575141.21742432786-0.07054248161174.83251967289-2.679638998074.520579790180.34898084-0.2015365020940.1220058096560.32694171088-0.2173349842030.264329619342-0.347970542358-0.0607689181018-0.1685252751060.2784529959250.02621790135320.001471756073380.358708433515-0.00936666664650.28899558503737.78036382220.59938614547827.2546700042
156.20001961442-0.5285059019811.046172691811.19134526797-0.8717786544737.484352938120.114123585852-0.384639810377-0.749853543850.0546940990558-0.2275611481860.1398699088380.584684406490.441725885597-0.01547796857770.2523073959940.004958533984590.02771272014410.2495397205570.04513306134090.27287395861240.6073418938-11.51057670326.2438968456
162.590597814950.790092308525-1.530507450174.41238756687-4.742759349296.74120657490.1035537446410.190143920827-0.303616261613-0.009959640618810.123041246010.1272369307650.238698726941-0.781053509372-0.1118201242020.300013394623-0.0555266112271-0.04669206475680.3659940862470.01965656075490.37906448178431.2466394353-7.222399202719.6588828441
172.124483799910.006859403664120.2886275805122.70093568615-2.847456479194.63381355508-0.0217064751709-0.39571060175-0.1021349257780.07874336811480.3791130628060.491669080085-0.132615256915-0.53948640653-0.3967859132790.2318527545270.04072765726240.01968963899950.4148486368120.03729053142720.28766863504430.5475732864-3.9499952712629.7684278605
180.234981466295-0.3693371241711.135768276551.88536293166-2.479725409364.09987858147-0.0908788259853-0.1274872515740.01449117187060.2804003929260.00810579322546-0.13788885839-0.236326069776-0.0611394756340.04144281253340.2815908746180.02130268784350.02584127174680.2941627264980.0006290011922370.28876487877946.0992623464-8.7786172461340.0979554158
193.696914978060.2801720456890.4874290127671.64679975683-2.022203687434.765398010950.1074820707290.130534730255-0.06535333156630.567221586209-0.0623082420421-0.359619479754-0.6181940999560.349755255988-0.01471853556510.414042840787-0.067410760616-0.05762122710310.2568337740030.008173445744510.33387345696451.3548348672-12.63530509653.5962666161
207.662972070831.783752643593.754078410781.943129484390.4064764382825.24778673231-0.415484342124-0.1060286970010.4692713755480.4567146003620.232993380780.0164955691893-1.291011185110.2084058004960.198018171410.782367348621-0.0212194309296-0.006469346394040.3691629175740.03214272583080.43164028737650.1933800202-5.9159016679759.5075997792
218.32148241083-0.12681953283.306240656994.811684391521.06201783347.44834378668-0.684302519524-1.216929872660.3659057473671.707124836430.4560906204760.0360036845889-1.31267537332-0.65909211470.08060207521310.9030848977820.04931555606350.04955093205830.408205787713-0.01894942378640.35377768204349.3158975046-9.8572116769165.2618496398
225.66402736871-0.1917001321211.951993915342.5875298759-1.02727120383.014689346820.264693496263-0.312795973668-0.0318496785582-0.567055409262-0.595694717287-0.2184881711871.029593025480.4401551513640.3093466452690.4076258361390.2155557032810.08624197551410.5028764886850.07939632323890.46156444918158.9844081875-17.077396202721.122653123
233.16951262097-0.4527167336570.7622090067192.99469958572-0.6288262066258.109079123930.2947146281730.268160665242-0.105205971046-0.266308140647-0.134739471540.03583556152240.430246226690.382808925188-0.1532326540320.3198993738030.08161652750670.0182373389850.3604702309440.02842618065520.29184616610251.4037712831-9.3236968360115.446988332
242.93270726917-1.122836915580.8539327173712.8650071897-1.683493224093.645889992820.0784986663618-0.0265417080538-0.111850311078-0.126559058408-0.173135498609-0.31566104498-0.1449399651160.631942247970.1939806495670.2642390217240.03746738933240.03190419572850.485866084950.09020322650290.36502134948258.2266580199-5.7715198569920.5359885013
254.23236597588-0.8061408311821.024364936031.61951377389-0.9019384889194.30924070316-0.217889326197-0.198660184696-0.218177422874-0.0914063063953-0.113453362437-0.0714522249603-0.1161935171630.3602001926840.1795376912510.3472192435580.06201257291580.04181471424790.3237921328550.06506741870450.29645505320553.8869236086-10.695083999623.2492255193
261.79061306694-1.448972529242.196187642331.24030333583-1.906429645492.728184496030.4505775734040.4673871005780.146510858451-0.516793093466-0.870425907908-0.7098651211710.990438992791.152753048070.318091107480.3765602402850.0774845291684-0.02515235251650.8076559409860.3268109399990.56572852872567.092618355-18.444751033637.3398963118
275.026194804410.0925685912505-1.59278281023.65563985333-2.706442133526.4759680137-0.0546974576064-0.046487969350.2451031434490.362232440784-0.0200522379651-0.034034296126-0.07232547726990.3133110485680.04791626096760.362166559888-0.0120535658427-0.1428908579970.2937425754660.03451081819030.31363406407556.395175745-24.130656505255.9084606656
281.420592476460.302556898459-1.384796047239.37600770526-6.049368606664.8915690538-0.223403744734-0.104872727063-0.120585389697-0.2515063400770.1583266140480.0732719087720.185911707087-0.2600574093640.05649843885820.438146638820.00565315913306-0.1361628421810.378357607235-0.04994240581460.37915861196552.9264516285-32.1380805252.9726029834
295.368380337530.200096773513-1.938379785023.16005642709-1.70762675915.22849214744-0.1754316576-0.00380928534252-0.01740462393640.395279062244-0.051427430567-0.2532260869130.1051518475780.1123658603290.1881227231660.334575086172-0.0269658665994-0.1346778130570.3036003496040.001012160653720.34145695540458.7664700568-26.463442692955.9023105522
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 333 through 349 )EA333 - 3491 - 17
22chain 'E' and (resid 350 through 409 )EA350 - 40918 - 77
33chain 'E' and (resid 410 through 469 )EA410 - 46978 - 137
44chain 'E' and (resid 470 through 518 )EA470 - 518138 - 186
55chain 'A' and (resid 1 through 17 )AD1 - 171 - 17
66chain 'A' and (resid 18 through 25 )AD18 - 2518 - 25
77chain 'A' and (resid 26 through 44 )AD26 - 4426 - 44
88chain 'A' and (resid 45 through 60 )AD45 - 6045 - 60
99chain 'A' and (resid 61 through 83 )AD61 - 8361 - 83
1010chain 'A' and (resid 84 through 99 )AD84 - 9984 - 99
1111chain 'A' and (resid 100 through 117 )AD100 - 117100 - 117
1212chain 'A' and (resid 118 through 124 )AD118 - 124118 - 124
1313chain 'H' and (resid 1 through 17 )HF1 - 171 - 17
1414chain 'H' and (resid 18 through 39 )HF18 - 3918 - 39
1515chain 'H' and (resid 40 through 51 )HF40 - 5140 - 51
1616chain 'H' and (resid 52 through 66 )HF52 - 6652 - 66
1717chain 'H' and (resid 67 through 90 )HF67 - 9067 - 90
1818chain 'H' and (resid 91 through 139 )HF91 - 13991 - 139
1919chain 'H' and (resid 140 through 193 )HF140 - 193140 - 193
2020chain 'H' and (resid 194 through 208 )HF194 - 208194 - 208
2121chain 'H' and (resid 209 through 221 )HF209 - 221209 - 221
2222chain 'L' and (resid 1 through 25 )LG1 - 251 - 25
2323chain 'L' and (resid 26 through 38 )LG26 - 3826 - 38
2424chain 'L' and (resid 39 through 75 )LG39 - 7539 - 75
2525chain 'L' and (resid 76 through 101 )LG76 - 10176 - 101
2626chain 'L' and (resid 102 through 113 )LG102 - 113102 - 113
2727chain 'L' and (resid 114 through 150 )LG114 - 150114 - 150
2828chain 'L' and (resid 151 through 163 )LG151 - 163151 - 163
2929chain 'L' and (resid 164 through 214 )LG164 - 214164 - 214

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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