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- PDB-7bem: 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: 7bem
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 scFv
要素
  • COVOX-269 Vh domain
  • COVOX-269 Vl domain
  • Spike glycoprotein
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / germline / V-gene / receptor-binding-domain / spike / neutralisation / protection / glycosylation / valency / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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, 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
PHOSPHATE ION / PROLINE / 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: 2.52 Å
データ登録者Zhou, D. / Zhao, Y. / Ren, J. / Stuart, D.
資金援助 英国, 中国, 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 中国
引用ジャーナル: Cell / 年: 2021
タイトル: The antigenic anatomy of SARS-CoV-2 receptor binding domain.
著者: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / ...著者: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / Guido C Paesen / Jose Slon-Campos / César López-Camacho / Natasha M Kafai / Adam L Bailey / Rita E Chen / Baoling Ying / Craig Thompson / Jai Bolton / Alex Fyfe / Sunetra Gupta / Tiong Kit Tan / Javier Gilbert-Jaramillo / William James / Michael Knight / Miles W Carroll / Donal Skelly / Christina Dold / Yanchun Peng / Robert Levin / Tao Dong / Andrew J Pollard / Julian C Knight / Paul Klenerman / Nigel Temperton / David R Hall / Mark A Williams / Neil G Paterson / Felicity K R Bertram / C Alistair Siebert / Daniel K Clare / Andrew Howe / Julika Radecke / Yun Song / Alain R Townsend / Kuan-Ying A Huang / Elizabeth E Fry / Juthathip Mongkolsapaya / Michael S Diamond / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and ...Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
履歴
登録2020年12月24日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年3月3日Provider: repository / タイプ: Initial release
改定 1.12021年4月7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 / _citation_author.name
改定 1.22021年4月28日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32024年1月31日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: COVOX-269 Vh domain
L: COVOX-269 Vl domain
E: Spike glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)54,13114
ポリマ－52,6543
非ポリマー1,47611
水59433
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 area6160 Å2
ΔGint-35 kcal/mol
Surface area18380 Å2
手法PISA
単位格子
Length a, b, c (Å)173.614, 173.614, 120.642
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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要素

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抗体 , 2種, 2分子 HL

#1: 抗体 COVOX-269 Vh domain


分子量: 13950.331 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 COVOX-269 Vl domain


分子量: 15553.229 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

#3: タンパク質 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


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
#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...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: 570.542 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
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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非ポリマー , 5種, 43分子

#5: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#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
#8: 化合物
ChemComp-PRO / PROLINE / プロリン


タイプ: L-peptide linking / 分子量: 115.130 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C5H9NO2
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 33 / 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: 4.99 Å3/Da / 溶媒含有率: 75.33 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M Proline, 0.1 M HEPES pH 7.5 and 10% (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: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年11月25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: 0.97625 Å / 相対比: 1
反射解像度: 2.52→57 Å / Num. obs: 36739 / % possible obs: 99.9 % / 冗長度: 73.4 % / Biso Wilson estimate: 70.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.432 / Rpim(I) all: 0.051 / Net I/σ(I): 9.2
反射 シェル解像度: 2.52→2.56 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1714 / CC1/2: 0.627

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解析

ソフトウェア
名称バージョン分類
GDA1.18.1_3865データ収集
PHENIX1.18.1_3865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: 7BES

7bes


解像度: 2.52→47.05 Å / SU ML: 0.5343 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 34.1414
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2469 1753 4.92 %
Rwork0.2169 33912 -
obs0.2184 35665 96.99 %
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: 93.8 Å2
精密化ステップサイクル: LAST / 解像度: 2.52→47.05 Å
タンパク質核酸リガンド溶媒全体
原子数3197 0 94 33 3324
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00443363
X-RAY DIFFRACTIONf_angle_d0.64234561
X-RAY DIFFRACTIONf_chiral_restr0.0444497
X-RAY DIFFRACTIONf_plane_restr0.004583
X-RAY DIFFRACTIONf_dihedral_angle_d15.34311203
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.4326980.43061901X-RAY DIFFRACTION72.8
2.58-2.660.42521030.42172456X-RAY DIFFRACTION92.08
2.66-2.750.41351380.39632637X-RAY DIFFRACTION99.46
2.75-2.840.37541280.36262610X-RAY DIFFRACTION99.1
2.84-2.960.45921490.35962615X-RAY DIFFRACTION99.21
2.96-3.090.36911390.3412643X-RAY DIFFRACTION98.86
3.09-3.260.33171300.28552649X-RAY DIFFRACTION99.43
3.26-3.460.30311530.24122665X-RAY DIFFRACTION99.89
3.46-3.730.25021380.22332663X-RAY DIFFRACTION99.82
3.73-4.10.23861170.17952709X-RAY DIFFRACTION99.68
4.1-4.70.18771500.14412720X-RAY DIFFRACTION99.86
4.7-5.910.16771490.15482736X-RAY DIFFRACTION99.93
5.91-47.050.1991610.18932908X-RAY DIFFRACTION99.9
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)
15.85297414772.828389436234.656219077988.155760787741.304116505733.83923316659-1.40459828042-1.180659034610.7755559881051.151096559951.085902596220.387342863067-0.2699858653780.5291815543930.4390521087620.693605698412-0.04337812003490.01998860378470.855913146984-0.03022509085710.68629212397765.6936625717-45.5705745612-8.90789641747
21.82362738524-0.667183411678-3.165002942365.04829249081.037721299295.64314962520.53486057334-0.345211336834-0.2322145232860.548847747012-0.502532462164-0.533989152857-0.4231784367530.2140688362770.00216868346060.970764955018-0.0529771746664-0.1277209596691.11968674843-0.1045824344560.64714461902589.1212184626-50.8840863337-7.78754231973
38.663595592391.519735317150.9957256085632.577336659052.650273501886.900714094940.672378681894-0.7334552168040.04466748179870.392074200641-0.665120551047-0.132714761919-0.28717089055-0.1032268177410.1134954743890.815100633873-0.0601435712391-0.09600396195430.8319707190460.01092767040180.5734120659867.2727419933-51.7326752114-2.74806208882
44.846256965370.0226022891114-1.049777775110.867866930925-0.3664758864130.364137125483-0.502225389007-0.802931720947-0.480657148429-0.282096318994-0.114159195828-0.2232387108361.07622325823-0.146041419510.05767646766440.628994319161-0.154930373769-0.04192315513930.8087629710460.01539372885240.49877937520571.2154476261-57.7068701359-10.8365793893
53.020629184641.07004428497-0.8315934067334.02151507149-2.834765269232.87021430216-0.2709117820661.05773529191-0.333598821241-1.06248148691-0.2164072291540.164548691491-0.530611193712-0.623805873960.288767423580.754050837023-0.00394094285094-0.05132531375430.795093759330.01034662721210.44867193780775.459306038-59.78253306-15.0022934424
64.16222451133-0.350952726206-1.354530089533.62885201395-0.6329304245612.95233630060.1045356797570.000486563799966-0.547090334367-0.58229603738-0.1725623600020.6079688614260.829360965346-0.6231079532370.09610272310030.747312382524-0.124041844782-0.08076125436840.915342793892-0.01409292898670.62558414169672.4394582899-65.4500753583-4.40908412887
74.57293740937-0.553595908976-0.5527469296662.33673293654-1.097744859141.44093756118-0.205475844663-0.4879383081130.0154422616496-0.765687280780.1828072238810.4034687112310.1145094038810.2455598447050.2636224501460.7137586136130.0774475577597-0.1037621575380.860698426070.02655986311740.68397462377476.8286813194-59.6391067317-1.91873245916
87.73611089965-4.33377910207-1.179191251075.23759823381.122481240192.44913859190.370615646212-0.9508091675740.3329342316280.591250681945-0.347428884531-0.0307855012853-0.146105704578-0.2727883505450.1096244655920.947142766828-0.1119081634760.1101921581020.958944329767-0.06433574871520.59366300899372.27613251-52.10124752370.0285618099351
93.878781145362.29839047573-1.268860077292.73358169843-2.175453626737.62380878910.05527942299790.316008093751-1.88733120045-0.5345055344020.540917719453-0.412169232490.5579750109230.6711521389590.3834393794690.893484672563-0.1333103999810.01651894782320.990792504641-0.01661955059640.64607965905587.188982829-58.4243113592-10.8230900498
103.033279761421.48611039797-3.160921697751.95548257275-0.2682767988424.32667945769-0.321820457050.7815250986870.8580394106070.05222666266010.1229956567530.232456096652-0.139440956454-0.04987656340030.2526236086420.732899531022-0.102907982216-0.0612236162940.8104021762560.01485370557660.60254752435370.8862348907-54.1903847994-12.4379058178
118.207128755867.60798625865-1.286779002618.21825505150.167729805684.90138921092-0.41559344860.2758869496050.442772718450.1370290405570.256019558154-0.2773745728750.529403378667-0.6181164998340.2342120885930.666366206076-0.0673904607186-0.02118104082540.768043352068-0.05326220285620.56528102890361.3906866295-58.8580190246-13.8925610365
129.21282807083.140723606260.4597218327614.65236024815-0.721464546713.352765481170.0552986155771-0.61070485375-0.0037583960115-0.55311330775-0.1972868191860.13689628392-0.4295840621250.360139091330.2211172666240.7975613813260.02070677177420.0003848863954970.983915149522-0.04118123011850.52625698557382.388712557-49.1696604083-13.8193846028
131.37325540608-1.251918096531.216990439675.14923376735-5.23749630555.34385021545-0.3876774201070.0794662181323-1.142094708170.218631655364-0.486875937103-0.9974750432751.148303179631.197235067350.6140409070411.221015215960.07065325853090.02463937829051.030702013430.04686189216580.71041244575471.0446870605-71.2941960763-25.1587403275
143.180146346530.402448023266-0.7433115157662.57577946258-1.508899345153.68061624987-0.05422926689960.3344685786030.147145510787-0.801107045157-0.1019311025840.2579285931760.1663649919430.05330894630430.1064362855030.810291123454-0.019221509605-0.09628606151010.792499095526-0.03097593273510.49681297469161.8337086233-60.1999691267-28.3927335189
154.302679418324.803318397220.4096242133885.550828450050.5424975026610.42022483506-0.1298437157060.2829046174261.40167504529-0.0438931589358-0.7199234601680.99185768823-0.935994434736-0.380828051968-0.407995229880.9426411878840.00347292714251-0.1384659132370.9217023845710.04164688300840.87137216597562.3391698454-48.8528701415-34.8496174568
166.89194004171.903850446670.1307813753347.339010190744.518005558793.24527309644-0.0195832700996-0.159670968601-0.5579096354580.0113165964121-0.178355388127-0.1070762578030.3175994848860.3109539532410.1395130052010.667639622079-0.0889589049051-0.0349094212730.8348925174070.06879609228990.63773578041468.1962514399-64.8651396781-20.56688789
172.141680058691.45123009879-1.324411873982.90352242061.062539848872.842098171930.125035238576-0.1171783877620.546460350457-0.0619907149852-0.869564055293-0.654748223386-2.637869036012.791014933320.8297107090711.27297902826-0.1687821121980.08457494741760.8618063740920.1277145754750.6860295551270.3809355462-51.0107263119-38.3751725636
184.29578263117-3.054649708971.271924272589.14054041279-1.859785193486.438135745760.323162877616-0.343137864084-0.4815780977180.406791591278-0.336303391004-0.5883657017330.6111607642970.00238004618931-0.0659035535240.843825669261-0.155876954849-0.01559559575870.9857099044060.1279297230650.81086932680755.9377673771-93.01124503620.618169685543
198.76199173117-3.046355312988.393659607576.425649253-2.224328960698.162847306120.1165009701920.607764298736-1.091219683411.604179378570.4106461621640.868098540702-0.0543916656453-0.21897574907-0.4401109885131.186307281820.0192485842351-0.0462148375771.407856530710.4901045898711.212889261864.9266690096-97.8046536410.2060681994
204.223117327371.614316965181.136249285996.587361295541.655711758774.50164030280.320949927531-0.573527819688-0.2472497147460.686844712523-0.213412202996-0.1508220269020.305002920266-0.0140757336882-0.1578601588220.729879753929-0.10669892785-0.009243727000640.9132584028860.08784019111580.59099140305961.2989348432-81.677269519-1.9320765348
212.411516324110.212322906421-0.4921457395823.655296088643.413990085074.63775819579-0.0319224580446-0.442280740709-0.157145250540.21461336357-0.7045618126860.918572203537-0.0706625301403-0.3196035565390.6997490515150.781698619655-0.0253370536754-0.09136542198170.8940950074580.03898883054120.61808708330853.5188949837-73.3309095963-3.77408113654
222.22921294073-1.277958462291.536022341519.84207082655-0.7228674360921.01072975709-0.0306509155861-0.0542766407760.1439997173050.197884524312-0.4018843419820.721122889079-0.38741981435-0.5320416721460.3488076039310.837647267996-0.02322098082390.00434258222451.08858908403-0.1053394840050.66191314309949.9004826006-58.5673162467-4.91805585637
232.741250673413.441531945610.8821298188516.495541488272.909143750651.739336195690.008836468093880.06446933015210.498570737873-0.401173696147-0.123951957236-0.538744563953-0.3529512738880.02135405247120.1462902299130.85616412997-0.0670343564748-0.1233574889840.810214300405-0.09375651731310.8033523877158.4340399481-79.4439522895-18.0948475094
247.66780545243-3.433759319864.199333216193.22502685217-3.504367601663.96854780972-0.788131142478-1.983130339610.1595021848061.382902317990.109843140316-0.181534487238-0.4386011606660.1714358688440.5476296632770.966930882186-0.0347910152396-0.07793209181421.094680191830.06155379308110.80788503413859.9768100965-89.09402535273.81350913109
250.4108366323280.3596179080730.09581693419970.2615774650510.00145586341521-0.0586690658201-0.774062662530.930381256364-0.341337958981.053992757840.470769567862-0.764397696827-0.2247004142750.0102339669510.0003646663268761.747685411440.1390450992720.03956028568511.57157304981-0.06683189550121.9654559796360.434442377-76.3738105131-6.37773794343
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 7 )HA1 - 71 - 7
22chain 'H' and (resid 8 through 17 )HA8 - 178 - 17
33chain 'H' and (resid 18 through 32 )HA18 - 3218 - 32
44chain 'H' and (resid 33 through 39 )HA33 - 3933 - 39
55chain 'H' and (resid 40 through 51 )HA40 - 5140 - 51
66chain 'H' and (resid 52 through 63 )HA52 - 6352 - 63
77chain 'H' and (resid 64 through 72 )HA64 - 7264 - 72
88chain 'H' and (resid 73 through 82 )HA73 - 8273 - 82
99chain 'H' and (resid 83 through 90 )HA83 - 9083 - 90
1010chain 'H' and (resid 91 through 98 )HA91 - 9891 - 98
1111chain 'H' and (resid 99 through 107 )HA99 - 10799 - 107
1212chain 'H' and (resid 108 through 117 )HA108 - 117108 - 117
1313chain 'L' and (resid 0 through 7 )LC0 - 71 - 8
1414chain 'L' and (resid 8 through 75 )LC8 - 759 - 76
1515chain 'L' and (resid 76 through 84 )LC76 - 8477 - 85
1616chain 'L' and (resid 85 through 103 )LC85 - 10386 - 104
1717chain 'L' and (resid 104 through 109 )LC104 - 109105 - 110
1818chain 'E' and (resid 334 through 380 )ED334 - 3801 - 47
1919chain 'E' and (resid 381 through 394 )ED381 - 39448 - 61
2020chain 'E' and (resid 395 through 442 )ED395 - 44262 - 109
2121chain 'E' and (resid 443 through 469 )ED443 - 469110 - 136
2222chain 'E' and (resid 470 through 494 )ED470 - 494137 - 161
2323chain 'E' and (resid 495 through 506 )ED495 - 506162 - 173
2424chain 'E' and (resid 507 through 519 )ED507 - 519174 - 186
2525chain 'E' and (resid 1301 through 1601 )EH1301 - 16015 - 8

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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