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- PDB-7beo: 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: 7beo
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs
要素
  • (COVOX-253H55L ...) x 2
  • COVOX-75 heavy chain
  • COVOX-75 light chain
  • 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


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
類似検索 - ドメイン・相同性
ACETATE 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: 3.19 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 1.32023年11月29日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name
改定 1.42024年1月31日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
R: Spike glycoprotein
H: COVOX-253H55L heavy chain
L: COVOX-253H55L light chain
A: COVOX-75 heavy chain
B: COVOX-75 light chain
X: Spike glycoprotein
C: COVOX-253H55L heavy chain
D: COVOX-253H55L light chain
E: COVOX-75 heavy chain
F: COVOX-75 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)246,04026
ポリマ－243,35610
非ポリマー2,68416
水00
1
R: Spike glycoprotein
H: COVOX-253H55L heavy chain
L: COVOX-253H55L light chain
A: COVOX-75 heavy chain
B: COVOX-75 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,79812
ポリマ－121,6785
非ポリマー1,1207
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
X: Spike glycoprotein
C: COVOX-253H55L heavy chain
D: COVOX-253H55L light chain
E: COVOX-75 heavy chain
F: COVOX-75 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,24214
ポリマ－121,6785
非ポリマー1,5649
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)93.421, 150.070, 116.080
Angle α, β, γ (deg.)90.000, 91.979, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 192 or resid 194 through 228 or resid 501))
d_2ens_1(chain "E" and (resid 1 through 192 or resid 194 through 228 or resid 401))
d_1ens_2(chain "B" and (resid 1 through 17 or resid 19 through 162 or resid 164 through 213))
d_2ens_2(chain "F" and (resid 1 through 17 or resid 19 through 162 or resid 164 through 213))
d_1ens_3(chain "C" and (resid 1 through 224 or resid 300 through 401))
d_2ens_3(chain "H" and (resid 1 through 224 or resid 300 through 401))
d_1ens_4(chain "D" and (resid 1 through 17 or resid 19...
d_2ens_4(chain "L" and (resid 1 through 17 or resid 19...
d_1ens_5(chain "R" and (resid 336 through 345 or resid 347 through 516))
d_2ens_5(chain "X" and (resid 336 through 345 or resid 347 through 516))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLEUJ1 - 188
d_12ens_1SERLYSJ192 - 226
d_13ens_1ACTACTL
d_21ens_1GLNLEUE1 - 188
d_22ens_1SERLYSE192 - 226
d_23ens_1ACTACTF
d_11ens_2ASPASPM1 - 17
d_12ens_2VALSERM19 - 162
d_13ens_2THRGLUM166 - 215
d_21ens_2ASPASPF1 - 17
d_22ens_2VALSERF19 - 162
d_23ens_2THRGLUF164 - 213
d_11ens_3GLNLYST1 - 219
d_12ens_3FUCFUCU
d_13ens_3NAGNAGV
d_14ens_3NAGNAGW
d_21ens_3GLNLYSC1 - 219
d_22ens_3FUCFUCD
d_23ens_3NAGNAGE
d_24ens_3NAGNAGF
d_11ens_4ASPGLUY1 - 17
d_12ens_4ALASERY19 - 163
d_13ens_4THRALAY167 - 196
d_14ens_4GLUGLUY200 - 218
d_15ens_4ACTACTZ
d_21ens_4ASPGLUH1 - 17
d_22ens_4ALASERH19 - 163
d_23ens_4THRALAH167 - 196
d_24ens_4GLUGLUH200 - 218
d_25ens_4ACTACTI
d_11ens_5CYSTHRA3 - 12
d_12ens_5PHEGLUA14 - 183
d_21ens_5CYSTHRO2 - 11
d_22ens_5PHEGLUO13 - 182

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(-0.99998240968, 0.00589978741174, -0.000610604943787), (-0.00590489145484, -0.999944500625, 0.00872513192322), (-0.000559094632108, 0.00872858400128, 0.999961748886)-46.767866497, -0.507140590106, -0.200893584323
2given(-0.999993460239, 0.0027340903468, -0.00236732543772), (-0.00275228491473, -0.99996643689, 0.00771686601591), (-0.00234614737404, 0.00772333110353, 0.999967422344)-46.7226724839, -0.493240675774, -0.150775954996
3given(-0.999992766273, -0.00371274536381, -0.000826391776451), (0.00370776045163, -0.999975400431, 0.00595407808188), (-0.000848477423364, 0.00595097094896, 0.999981932852)-46.9721932114, -0.325018295827, 0.0661948689963
4given(-0.999997944705, -0.00196667970993, -0.000492702999272), (0.00196115869018, -0.999937947703, 0.0109660658124), (-0.00051423916505, 0.0109650770051, 0.999939749507)-46.9428914992, -0.601869910735, 0.108940733249
5given(-0.999980291554, 0.00383311278441, -0.00497229832593), (-0.00387284596789, -0.999960451362, 0.00800604619579), (-0.00494141360028, 0.00802514535458, 0.999955588751)-46.7720716443, -0.54118139469, -0.161345466491

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要素

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タンパク質 , 1種, 2分子 RX

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


分子量: 23150.891 Da / 分子数: 2 / 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

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抗体 , 4種, 8分子 HCLDAEBF

#2: 抗体 COVOX-253H55L heavy chain


分子量: 24371.400 Da / 分子数: 2 / 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 COVOX-253H55L light chain


分子量: 23465.938 Da / 分子数: 2 / 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 COVOX-75 heavy chain


分子量: 26133.400 Da / 分子数: 2 / 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 COVOX-75 light chain


分子量: 24556.418 Da / 分子数: 2 / 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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糖 , 2種, 4分子

#6: 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: 3 / 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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 / タイプ: SUBJECT OF INVESTIGATION
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 , 3種, 12分子

#8: 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
#9: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C2H3O2
#10: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl

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詳細

研究の焦点であるリガンドがあるかY

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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: 3.34 Å3/Da / 溶媒含有率: 63.19 %
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 / pH: 5.5
詳細: 0.1 M ammonium acetate, 0.1 M bis-Tris pH 5.5 and 17% (w/v) PEG 10000

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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27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: 3.19→66.4 Å / Num. obs: 53225 / % possible obs: 100 % / 冗長度: 6.9 % / Biso Wilson estimate: 78.74 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.412 / Net I/σ(I): 4
反射 シェル解像度: 3.19→3.25 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2657 / CC1/2: 0.28

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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: 7BEN

7ben


解像度: 3.19→58.01 Å / SU ML: 0.5262 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.9557
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2735 2657 5.01 %
Rwork0.2341 50411 -
obs0.2361 53068 99.72 %
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: 90.21 Å2
精密化ステップサイクル: LAST / 解像度: 3.19→58.01 Å
タンパク質核酸リガンド溶媒全体
原子数16112 0 177 0 16289
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001916694
X-RAY DIFFRACTIONf_angle_d0.503822720
X-RAY DIFFRACTIONf_chiral_restr0.04242565
X-RAY DIFFRACTIONf_plane_restr0.00422917
X-RAY DIFFRACTIONf_dihedral_angle_d18.54415971
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2JX-RAY DIFFRACTIONTorsion NCS0.157573507827
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS0.140701689214
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.171744163256
ens_4d_2LX-RAY DIFFRACTIONTorsion NCS0.163329889309
ens_5d_2AX-RAY DIFFRACTIONTorsion NCS0.243726232859
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.250.40941580.38322579X-RAY DIFFRACTION97.58
3.25-3.310.36981210.34172646X-RAY DIFFRACTION99.86
3.31-3.380.37811460.3092658X-RAY DIFFRACTION99.79
3.38-3.450.3241330.30572642X-RAY DIFFRACTION99.78
3.45-3.530.33041290.28282647X-RAY DIFFRACTION99.82
3.53-3.620.3261320.28822656X-RAY DIFFRACTION99.89
3.62-3.720.27661340.272651X-RAY DIFFRACTION99.86
3.72-3.830.28931400.25982631X-RAY DIFFRACTION99.86
3.83-3.950.31561330.26042666X-RAY DIFFRACTION99.79
3.95-4.090.28771190.23362658X-RAY DIFFRACTION99.71
4.09-4.260.2511610.22142651X-RAY DIFFRACTION99.86
4.26-4.450.24811490.20222652X-RAY DIFFRACTION99.93
4.45-4.690.24771250.19962665X-RAY DIFFRACTION100
4.69-4.980.23431310.19082661X-RAY DIFFRACTION99.89
4.98-5.360.22721500.18692639X-RAY DIFFRACTION99.89
5.36-5.90.23121680.1972649X-RAY DIFFRACTION100
5.9-6.760.26661600.21552645X-RAY DIFFRACTION99.93
6.76-8.510.25941250.22192711X-RAY DIFFRACTION100
8.51-58.010.26171430.21492704X-RAY DIFFRACTION99.34
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)
13.70039024267-0.97268909872-3.113711220074.13271039959-0.09170528698717.60362278573-0.1754986884580.02201740751040.1502538102480.06678280959920.866068177087-0.1218983383930.365719568701-0.0501261353422-0.6864764098330.466951091431-0.00342085052832-0.1228601044240.9839609509720.1102253742030.697168651977-50.44084118513.3920232051-23.811425406
22.53943919377-0.314787509046-2.67928929781.35133861202-0.2073742270523.01505916973-0.7647672331610.8046346560520.551924935299-0.528161196987-0.3307045423490.7241956495890.15319966786-0.4789557737180.973053169540.679764796843-0.0305715186723-0.4206075639870.894549438199-0.05301382244791.0898596865-51.454198861-5.43099194997-26.3551540651
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482.69523161855-0.34069235155-0.2162020937852.155476553361.560434314723.02740448221-0.0847826683508-1.20349458653-1.875980650081.16789296162-0.495952231270.471482583421-0.7334187869260.7667562644490.1883204667450.870893709005-0.3509351499280.01723364813451.113762925420.2272386023960.449458002244-25.5094650657-11.594427803762.3723801669
491.79085079586-1.1214188176-0.9069777241172.055150638421.136179219910.6076425171230.137453841608-0.432607753356-0.7870710399550.6531499742790.290511160165-0.082838758348-0.05285580378040.8530837704110.1229527740080.765448124876-0.158416702675-0.113024579321.181722842820.09237982275410.427857288462-18.3134188848-9.5802690444656.4919037293
501.902309838152.145940195231.018806675055.673478481712.472077207471.29848190426-0.218857467104-0.529127639572-1.90998391278-0.312675350410.670281148889-1.522446074740.3537596971860.5582058514060.1409357097280.7338147017280.311809829753-0.0254373607710.8383751682150.32393601091.3479260842916.1056854089-18.147453702446.8637006903
514.19210329470.129706223711-0.6418405397035.44173869720.5667971372154.09056139-0.354923744850.7011545810610.1771252612350.8456312881270.354711806098-0.85791475993-0.412381421313-0.28558594747-0.2664562874830.787502993398-0.1852056481350.1148470218960.9534777576640.2148598340930.9125378058236.25237559022-8.436273398753.3884814547
527.987028652632.4246170832-0.4588332534635.288787125340.3996034413822.886591946140.133475671769-0.279880806187-0.5489107147190.05725182355650.0554298035334-0.8641110479960.202901745053-0.0855732193389-0.2350000946440.717307775538-0.13309939614-0.04697758277170.7811020384680.01366060370630.7801099845028.42481248324-5.4619606459645.2905313811
534.18551361151.50527689612-3.253944384782.431566707510.5557013433824.122444446740.109836677832-2.58482230085-1.304801542761.17236758672-0.384621952819-1.288547994120.644913688102-0.5708905611330.03198053483861.02436875518-0.1265269761750.09944259667911.559521709620.5556583167231.02078823868-4.01860370814-15.771441232662.3472825054
546.56480171706-0.128247352631-1.173536709184.15790866010.7187935641314.022186438130.152444286858-0.119094787387-0.885798034668-0.08156639300930.00573654793949-1.07261844817-0.3441823433351.3247077627-0.3046595301270.649608606392-0.056709573366-0.06605198154440.914597407265-0.02211179807210.8252424084615.4253515514-8.7242376742944.7296267599
553.412893481661.601049623220.5379424001644.58653779591-0.1878204593035.014020599390.0124249770508-1.794048813130.0720040031050.606417169380.276492980201-1.28743118204-0.2734512757081.40197512682-0.3747235663520.704496078324-0.243850458406-0.2178604058191.26801881133-0.1036847694190.67438613418714.5762183381-5.3950139909656.6840699564
563.343865590991.846202425911.104384936712.14005031106-1.527017056525.142133969210.0518626484897-0.3049018939930.002289782240220.82888848228-0.38475853049-0.9275937744150.4407345240620.8589821947890.5012114385230.601392739424-0.0703265202152-0.1470403105150.4508417064030.04454948076750.822707894486-28.9314092245-8.099342078592.6341473809
577.063574951430.369934274092-5.061676614664.67519996281.479860001574.170436329350.533707934027-1.11609385158-0.3145739519170.9592226187260.0862636557143-0.523254344071-0.5231525041811.9063096202-0.008631456298090.703433345359-0.0402519306161-0.05151346741750.5732887782480.01012608289910.621250237721-30.8021376191-10.760624927916.1074938494
584.31521978983-0.861390984404-0.831612602622.008821725470.787503514516.442819423090.0432306430634-0.323595949374-0.1818538375440.106193727141-0.348751739563-0.5406652294370.7385854818820.442038081860.1586374011280.601951054072-0.03886027993550.03465798364420.4242793904360.1563433487860.688373344695-33.2665537968-17.73391639728.1378945201
591.183578263630.522807696752-1.087516563061.28415466235-0.5095390435962.148941988040.1318239754560.208377530767-0.315779204479-0.16922507573-0.05106353866890.2817411358530.347760297750.1399114881590.07024409371050.3917906042460.0207094879391-0.03561956647720.510324548880.04738387842960.56702173833-38.7897618596-8.08770985430.529813200482
603.41480849703-1.27920313197-0.2545664174154.68307492830.7292339128533.78260514046-0.13199114459-0.07939513939810.351202085217-0.3442829636560.5629759178640.554182022648-0.391742608786-0.36692816735-0.414160568410.4804830968480.03487885625870.08323297094720.4920339976920.1027074646040.650827398303-42.03317716269.0350195635-16.2355929891
612.49007340368-1.008051843640.2607920457891.431028571720.2345717480260.1151637320070.6409733439990.4477695287970.187739691017-0.107015185-0.33190533190.113372216969-0.533500801855-0.0984101713129-0.5091598542380.6027270117350.05071644776570.1429855323830.748026470686-0.004838936124760.718334247007-33.502754675610.9178756868-14.3172548437
622.01512732025-1.74960127828-2.287218775873.996150633092.065433069992.55038185637-0.5053898334680.32609104515-0.0992307098716-0.5533158056760.475925832223-0.114237195154-0.5286119138980.552013625214-0.2830393292330.64147070636-0.08666359760790.0319260606740.6180371647280.1385154315720.420866443669-34.815878334714.8938000964-21.0557529887
631.79500227083-0.5054391112842.285550334242.36036688774-1.627513036574.038667217170.2649610634450.0792737526902-0.0490853519534-0.8161885121180.196951205034-0.09386377918370.149129209125-1.37501073219-0.622401575840.674961116641-0.06241945394570.0759711257460.848928598510.3882961794290.834046778453-60.2411824668-10.31477409523.6356298573
645.0270390916-0.9470997274390.6174734571992.7114442868-2.251038531035.25280337883-0.0158937058397-0.545854001549-0.3058519467190.1930787069770.4736970596590.862902527773-0.199509761306-1.09473744845-0.4624364760040.5017956901080.03649319959490.103415509320.6264342588410.1056765982040.59355080976-55.3107027852-11.723709924412.4863318948
654.09282413533-0.7197799847780.4681521657361.89033550298-2.004665980533.678402722660.1582756790640.4860408922770.0008689868236230.6825117020020.03748872842180.879564898546-0.555452106018-0.675281139009-0.4040546647250.6401198903490.005713539766590.09218185021450.354443966301-0.02353312782960.567140818676-55.5940591001-6.626017726763.94639075914
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 'F' and (resid 114 through 150 )FF114 - 150114 - 150
22chain 'F' and (resid 151 through 163 )FF151 - 163151 - 163
33chain 'F' and (resid 164 through 213 )FF164 - 213164 - 213
44chain 'R' and (resid 334 through 353 )RA334 - 3531 - 20
55chain 'R' and (resid 354 through 380 )RA354 - 38021 - 47
66chain 'R' and (resid 381 through 469 )RA381 - 46948 - 136
77chain 'R' and (resid 470 through 516 )RA470 - 516137 - 183
88chain 'H' and (resid 1 through 39 )HC1 - 391 - 39
99chain 'H' and (resid 40 through 121 )HC40 - 12140 - 121
1010chain 'H' and (resid 122 through 167 )HC122 - 167122 - 162
1111chain 'H' and (resid 168 through 224 )HC168 - 224163 - 219
1212chain 'L' and (resid 1 through 30 )LH1 - 301 - 30
1313chain 'L' and (resid 31 through 76 )LH31 - 7631 - 76
1414chain 'L' and (resid 77 through 114 )LH77 - 11477 - 114
1515chain 'L' and (resid 115 through 129 )LH115 - 129115 - 129
1616chain 'L' and (resid 130 through 164 )LH130 - 164130 - 166
1717chain 'L' and (resid 165 through 175 )LH165 - 175167 - 177
1818chain 'L' and (resid 176 through 214 )LH176 - 214178 - 218
1919chain 'A' and (resid 1 through 17 )AJ1 - 171 - 17
2020chain 'A' and (resid 18 through 33 )AJ18 - 3318 - 33
2121chain 'A' and (resid 34 through 83 )AJ34 - 8334 - 83
2222chain 'A' and (resid 84 through 149 )AJ84 - 14984 - 145
2323chain 'A' and (resid 150 through 189 )AJ150 - 189146 - 185
2424chain 'A' and (resid 190 through 207 )AJ190 - 207186 - 205
2525chain 'A' and (resid 208 through 217 )AJ208 - 217206 - 215
2626chain 'A' and (resid 218 through 228 )AJ218 - 228216 - 226
2727chain 'B' and (resid 1 through 18 )BM1 - 181 - 18
2828chain 'B' and (resid 19 through 61 )BM19 - 6119 - 61
2929chain 'B' and (resid 62 through 90 )BM62 - 9062 - 90
3030chain 'B' and (resid 91 through 128 )BM91 - 12891 - 128
3131chain 'B' and (resid 129 through 150 )BM129 - 150129 - 150
3232chain 'B' and (resid 151 through 163 )BM151 - 163151 - 165
3333chain 'B' and (resid 164 through 198 )BM164 - 198166 - 200
3434chain 'B' and (resid 199 through 213 )BM199 - 213201 - 215
3535chain 'X' and (resid 335 through 353 )XO335 - 3531 - 19
3636chain 'X' and (resid 354 through 380 )XO354 - 38020 - 46
3737chain 'X' and (resid 381 through 393 )XO381 - 39347 - 59
3838chain 'X' and (resid 394 through 421 )XO394 - 42160 - 87
3939chain 'X' and (resid 422 through 469 )XO422 - 46988 - 135
4040chain 'X' and (resid 470 through 494 )XO470 - 494136 - 160
4141chain 'X' and (resid 495 through 516 )XO495 - 516161 - 182
4242chain 'C' and (resid 1 through 45 )CT1 - 451 - 45
4343chain 'C' and (resid 46 through 121 )CT46 - 12146 - 121
4444chain 'C' and (resid 122 through 200 )CT122 - 200122 - 195
4545chain 'C' and (resid 201 through 224 )CT201 - 224196 - 219
4646chain 'D' and (resid 1 through 30 )DY1 - 301 - 30
4747chain 'D' and (resid 31 through 62 )DY31 - 6231 - 62
4848chain 'D' and (resid 63 through 91 )DY63 - 9163 - 91
4949chain 'D' and (resid 92 through 114 )DY92 - 11492 - 114
5050chain 'D' and (resid 115 through 129 )DY115 - 129115 - 129
5151chain 'D' and (resid 130 through 151 )DY130 - 151130 - 151
5252chain 'D' and (resid 152 through 164 )DY152 - 164152 - 166
5353chain 'D' and (resid 165 through 175 )DY165 - 175167 - 177
5454chain 'D' and (resid 176 through 198 )DY176 - 198178 - 202
5555chain 'D' and (resid 199 through 214 )DY199 - 214203 - 218
5656chain 'E' and (resid 1 through 17 )EE1 - 171 - 17
5757chain 'E' and (resid 18 through 33 )EE18 - 3318 - 33
5858chain 'E' and (resid 34 through 83 )EE34 - 8334 - 83
5959chain 'E' and (resid 84 through 149 )EE84 - 14984 - 145
6060chain 'E' and (resid 150 through 207 )EE150 - 207146 - 205
6161chain 'E' and (resid 208 through 217 )EE208 - 217206 - 215
6262chain 'E' and (resid 218 through 228 )EE218 - 228216 - 226
6363chain 'F' and (resid 1 through 18 )FF1 - 181 - 18
6464chain 'F' and (resid 19 through 75 )FF19 - 7519 - 75
6565chain 'F' and (resid 76 through 113 )FF76 - 11376 - 113

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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