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- PDB-7bel: 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: 7bel
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs
要素
  • COVOX-45 heavy chain
  • COVOX-45 light chain
  • COVOX-88 heavy chain
  • COVOX-88 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
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: 2.53 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23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_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
R: Spike glycoprotein
A: COVOX-45 heavy chain
H: COVOX-88 heavy chain
L: COVOX-88 light chain
B: COVOX-45 light chain
X: Spike glycoprotein
C: COVOX-45 heavy chain
E: COVOX-88 heavy chain
F: COVOX-88 light chain
D: COVOX-45 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)247,14018
ポリマ－244,28310
非ポリマー2,8588
水2,648147
1
R: Spike glycoprotein
A: COVOX-45 heavy chain
H: COVOX-88 heavy chain
L: COVOX-88 light chain
B: COVOX-45 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,5879
ポリマ－122,1415
非ポリマー1,4454
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
X: Spike glycoprotein
C: COVOX-45 heavy chain
E: COVOX-88 heavy chain
F: COVOX-88 light chain
D: COVOX-45 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,5549
ポリマ－122,1415
非ポリマー1,4124
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)180.081, 140.721, 130.976
Angle α, β, γ (deg.)90.000, 124.557, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,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 186 or resid 188 through 222))
d_2ens_1(chain "C" and (resid 1 through 186 or resid 188 through 222))
d_1ens_2(chain "B" and (resid 1 through 162 or resid 164 through 193 or resid 195 through 213))
d_2ens_2(chain "D" and (resid 1 through 162 or resid 164 through 193 or resid 195 through 213))
d_1ens_3(chain "E" and (resid 1 through 12 or resid 14 through 128 or resid 301 through 306))
d_2ens_3(chain "H" and (resid 1 through 12 or resid 14 through 128 or resid 301 through 306))
d_1ens_4(chain "F" and ((resid 1 and (name N or name...
d_2ens_4(chain "L" and (resid 1 through 17 or resid 19 through 113))
d_1ens_5(chain "R" and (resid 334 through 518 or resid 520 through 527 or resid 601 or resid 801))
d_2ens_5(chain "X" and (resid 334 through 518 or resid 520 through 527 or resid 601 or resid 801))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLEUE1 - 180
d_12ens_1SERLYSE182 - 216
d_21ens_1GLNLEUS1 - 180
d_22ens_1SERLYSS184 - 218
d_11ens_2ASPSERN1 - 162
d_12ens_2THRALAN166 - 195
d_13ens_2GLUGLUN199 - 217
d_21ens_2ASPSERD1 - 162
d_22ens_2THRALAD166 - 195
d_23ens_2GLUGLUD199 - 217
d_11ens_3GLNVALT1 - 12
d_12ens_3PROALAT14 - 128
d_13ens_3NAGNAGU
d_14ens_3NAGNAGV
d_15ens_3BMABMAW
d_16ens_3MANMANX
d_17ens_3MANMANY
d_18ens_3MANMANZ
d_21ens_3GLNVALF1 - 12
d_22ens_3PROALAF14 - 128
d_23ens_3NAGNAGG
d_24ens_3NAGNAGH
d_25ens_3BMABMAI
d_26ens_3MANMANJ
d_27ens_3MANMANK
d_28ens_3MANMANL
d_11ens_4GLNARGF1 - 17
d_12ens_4THRPROF21 - 115
d_21ens_4GLNARGM1 - 17
d_22ens_4THRPROM21 - 115
d_11ens_5ASNLEUA1 - 185
d_12ens_5ALALYSA187 - 194
d_13ens_5ACTACTB
d_14ens_5NAGNAGD
d_21ens_5ASNLEUO1 - 185
d_22ens_5ALALYSO187 - 194
d_23ens_5ACTACTP
d_24ens_5NAGNAGR

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(-0.996076238276, -0.00951927198744, -0.0879858568298), (-0.0132769476985, 0.999020047063, 0.0422216558924), (0.0874977154048, 0.0432241717944, -0.995226517317)57.386410461, -2.8014614431, 56.0882599852
2given(-0.99610746492, 0.0100886585893, -0.0875679010759), (0.00839047557038, 0.999769955022, 0.0197392237668), (0.0877468988094, 0.0189276518111, -0.995962964043)58.6676791971, -1.5125427417, 54.4639805034
3given(-0.997124841664, -0.00477438609052, 0.0756257586654), (-0.00583343304566, 0.999887909804, -0.0137890857793), (-0.07555144734, -0.0141905977741, -0.997040924807)52.4202729781, 0.414484597472, 57.2354202588
4given(-0.997381365219, -0.0154644246449, 0.0706488774418), (-0.0168375491583, 0.999679934787, -0.0188818675428), (-0.070334267976, -0.0200219767746, -0.997322521151)52.3469405289, 0.728597384498, 57.0920116829
5given(-0.993479769703, -0.0298061763228, -0.110043350747), (-0.0263842843438, 0.999125946228, -0.0324224168389), (0.110913555214, -0.0293076001581, -0.993397829594)57.8433567277, 2.19624840138, 52.1094034521

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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 ACHELFBD

#2: 抗体 COVOX-45 heavy chain


分子量: 24187.152 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-88 heavy chain


分子量: 25853.088 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-88 light chain


分子量: 24278.861 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-45 light chain


分子量: 24671.332 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 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: 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: 2 / 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, 151分子

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


分子量: 59.044 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H3O2
#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: 1 / 由来タイプ: 合成 / 式: C3H8O3
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 147 / 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: 2.8 Å3/Da / 溶媒含有率: 56.03 % / 解説: presence of translational NCS
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: 8
詳細: 0.15 M (NH4)2SO4, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 4000

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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9月9日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97625 Å / 相対比: 1
反射解像度: 2.53→58.9 Å / Num. obs: 88040 / % possible obs: 97.8 % / 冗長度: 6.6 % / Biso Wilson estimate: 55.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.189 / Net I/σ(I): 5.6
反射 シェル解像度: 2.53→2.57 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 3392 / CC1/2: 0.326

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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: 7BEK

7bek


解像度: 2.53→49.41 Å / SU ML: 0.5174 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 38.0924
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2856 4193 4.91 %
Rwork0.2494 81143 -
obs0.2512 85336 94.82 %
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: 69.91 Å2
精密化ステップサイクル: LAST / 解像度: 2.53→49.41 Å
タンパク質核酸リガンド溶媒全体
原子数13206 0 190 147 13543
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002913740
X-RAY DIFFRACTIONf_angle_d0.611918710
X-RAY DIFFRACTIONf_chiral_restr0.04452113
X-RAY DIFFRACTIONf_plane_restr0.00412387
X-RAY DIFFRACTIONf_dihedral_angle_d16.76294932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.549314383232
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.439374797024
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.566106583483
ens_4d_2LX-RAY DIFFRACTIONTorsion NCS0.470736578244
ens_5d_2XX-RAY DIFFRACTIONTorsion NCS0.504513472543
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.550.4851560.42681398X-RAY DIFFRACTION48.45
2.55-2.580.4554810.42621711X-RAY DIFFRACTION60.03
2.58-2.620.43071050.40971834X-RAY DIFFRACTION65.13
2.62-2.650.44281270.40282365X-RAY DIFFRACTION81.89
2.65-2.680.47291380.39352637X-RAY DIFFRACTION95.36
2.68-2.720.39351590.40072830X-RAY DIFFRACTION98.32
2.72-2.760.40381300.37292833X-RAY DIFFRACTION99.16
2.76-2.80.40071370.37242824X-RAY DIFFRACTION100
2.8-2.850.40761570.35072834X-RAY DIFFRACTION100
2.85-2.890.39461320.32842836X-RAY DIFFRACTION100
2.89-2.940.36871290.31262891X-RAY DIFFRACTION99.97
2.94-2.990.36491320.3092841X-RAY DIFFRACTION99.9
3-3.050.3061350.32847X-RAY DIFFRACTION99.93
3.05-3.110.34021700.29212824X-RAY DIFFRACTION99.93
3.11-3.180.35791330.28012860X-RAY DIFFRACTION99.9
3.18-3.260.29621490.27042866X-RAY DIFFRACTION99.9
3.26-3.340.31421520.2612829X-RAY DIFFRACTION99.93
3.34-3.430.27951470.2632854X-RAY DIFFRACTION99.97
3.43-3.530.30821440.25052846X-RAY DIFFRACTION99.97
3.53-3.640.29131600.24022812X-RAY DIFFRACTION99.97
3.64-3.770.26921390.22212864X-RAY DIFFRACTION99.97
3.77-3.920.25371540.22442874X-RAY DIFFRACTION99.97
3.92-4.10.24361560.212836X-RAY DIFFRACTION99.9
4.1-4.320.23121470.1972836X-RAY DIFFRACTION99.97
4.32-4.590.2051620.18442861X-RAY DIFFRACTION99.97
4.59-4.940.22281410.18822848X-RAY DIFFRACTION99.83
4.94-5.440.23721490.20092885X-RAY DIFFRACTION99.87
5.44-6.230.26391460.22532855X-RAY DIFFRACTION99.9
6.23-7.840.25431630.23722861X-RAY DIFFRACTION99.9
7.84-49.410.28741630.23562851X-RAY DIFFRACTION97.67
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)
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483.44701135498-1.47882349966-3.149458108860.672716942691.411759949762.97693882144-0.4392136573630.1014374249780.6655562960850.2980854699840.831310454075-0.7989936598820.1090772329370.871040731558-0.3572948202770.630054754483-0.0430604778858-0.3867068809810.7039609105630.05223373122461.2210617589939.96328181.2104986744958.1814992088
496.655651920781.76233380924-1.396079568163.94425640553-1.229960080724.06287393158-0.06678479712810.5071563234281.62001166235-0.5768486168750.55346459153-0.7864085701820.06548531369610.934294087777-0.3039996222970.5288266592230.008762569079420.0662111253090.6623290864440.01576853853150.94373130488641.360019943-2.5550730012842.6837596864
505.533390679880.7093872277491.412730969564.313977157310.05127248267927.638702836870.637372695387-0.0429619064247-0.6289701702780.0797394122443-0.0666681174351-0.009234563305280.1968042500740.297703463301-0.6327068119350.4698846964660.0207634698729-0.1808223011730.465273702552-0.03690943665460.74121682179230.3720293311-6.5056463444151.837891602
513.31291321150.0569196108036-0.4282570866812.37349379973-0.8751194907178.40215727960.1038047447850.215450213836-0.629427270578-1.22558106122-0.285126794575-0.5300345304840.9646903449240.891894445450.2130883328080.6743749326160.0779590966633-0.05643958049050.614536967713-0.01734932946030.75637399944135.0851427416-2.2502989084142.015778738
520.637051399535-0.189478333410.1168976684421.172003084361.398683657685.040689848720.239043387982-0.459584189278-0.8934701404350.1123636557460.2208153388280.1737660087360.09038777827060.394580858717-0.538418837160.419764605454-0.00778374488864-0.2003397933420.6545189332260.1275727460040.88630309147231.8073790424-2.0113227377561.9674388385
533.805099943852.7423230207-3.378092101722.19297339369-3.555570363729.33224240390.5673402209980.1150072526450.1681029387870.2534219043880.9049231549470.501196567163-0.73896339312-0.382037244932-1.453423194970.6357828084450.174665700902-0.03835610766630.606155332085-0.2661948436591.1379763091938.72662368255.731869054841.8754631319
540.4092116058810.1603301674770.4960511496092.81045619483-0.2069478713870.599321543187-0.1205534598970.173130262520.233606233674-0.0733761548099-0.0868305953830.0653672713844-0.289684820817-0.498917755142-1.314443281550.141054559052-0.04568554810780.5635026932060.738810281605-0.00799993053235-0.55946950277416.3731870058-62.351668612352.4815072554
551.225415939930.644254337181-0.5450697707993.77116810981-0.3867566468381.00040633294-0.112203410832-0.4171458838040.289098899201-0.0767888218357-0.0219093256868-0.318627902440.137956737682-0.0748284595760.1106862383250.456736326057-0.0150713564351-0.1888888514090.5308581335370.03877164304380.76493982005126.3210067497-56.820400498752.1913122733
560.40608140080.847924837609-0.227288166542.09997079867-0.4034151952911.50869013274-0.1573502089360.09918296601370.175529523917-0.4810059258790.1268933628010.3920626906430.0552549110397-0.403042455839-0.06231261583580.37922706851-0.0460929774393-0.1451336067440.4583612539210.01985428475650.58621251001422.8428842508-57.956176703152.8386023039
570.7685461299620.5042995282980.08539507952371.8667692942-0.4523017314270.3950389010090.2038834519560.09410730711880.1301472722520.325997451674-0.4869773446360.209071988775-0.00561521865310.125438501033-0.3214353832310.517114119357-0.236453270730.5037214707850.5696937610890.002586748143410.047246016069916.7575497882-79.927149972554.3423440285
583.666084811-0.1623019622391.02661719672.547096088151.939510176977.453925483010.393651972962-0.995689366837-0.7875289180910.7611784941-0.31721386208-0.04579157316010.650250942960.544194959349-0.1390822943391.14941556824-0.360822833024-0.2756664682110.799891217550.1125159263370.66409085666220.4670395169-90.419168171982.331058195
593.55012046226-0.1299311200610.488127745833.892760622-1.272929248588.317703451180.134713220044-0.3342612371250.1409803419480.455307852523-0.05769703685110.2562513967350.432403319757-0.707804738095-0.140413488260.468357297249-0.0976397066179-0.1002305438090.42640024971-0.06232579270860.41128027712113.1098506548-84.272580772370.2413438065
607.626848960584.15015207912-2.23281950066.3207584974-3.456398042997.96098189160.0285210361805-0.0589337269993-0.3911416073670.4541923718030.4378158861140.0859063211870.184052196868-0.742057089388-0.549314639410.58590941955-0.0693360142822-0.07638369394660.7006448154860.0739319777940.5922747864498.73347049308-81.828848299577.855245155
612.940002235080.7878107573241.24526172482.7277565403-0.5011954745519.16893683560.325641237023-0.677563177616-0.575214265720.611808797675-0.286953509915-0.09815195930270.174640601425-0.654103555445-0.03246960807430.583195885204-0.12666903051-0.1146708454570.637166430746-0.05426477503010.41158108634914.6665474417-85.412338055874.1226795645
624.075615432511.578490874620.4482858743953.598163862070.2628321776768.890099262020.541766859983-0.903830643945-0.4859525024680.8864077123910.0441475608577-0.3559524318051.81842660879-1.37279348323-0.3346321188510.651815157328-0.276321126886-0.07847863438680.58528980756-0.04877092776650.6596435747929.48558372873-93.834618268972.0317777519
636.158969809582.8569673445-1.827011802695.57788509052-0.3496103748223.917739518140.535829158349-0.0861654582703-1.085025949950.664985165007-0.259700686949-0.4096372778850.01211176063810.105752726062-0.447189471250.4159467727890.139770714108-0.2026225640220.4918550433490.007806529335450.66466855860222.827674284-40.738460910913.4723732741
643.541494361061.480116588531.326510788422.48473314834-0.9536619140361.73930338888-0.00109044248378-0.451525707263-0.07775530124980.336357319002-0.0818471370254-0.180553159339-0.107212289747-0.05524831422350.0770404395840.4977988620110.0814270222522-0.04613811660170.4871404722-0.02383774944250.5593725374712.4923525932-34.828744017513.1300106236
650.939558602681.07809901228-1.365176205212.49148123165-0.3810810500072.94394553488-0.007282473529450.116489065693-0.254292311608-0.03943430313660.0614088303332-0.104803009391-0.1103401310630.36163894841-0.02870461983170.3788821423990.0403613054594-0.16620418750.401911356259-0.001059768929810.59372591055826.0068524493-26.92838535492.15849559579
661.56895141627-0.715784261693-1.901329894462.226492788380.1115503371084.287671937560.429314168912-0.4381249815970.1185124471230.0165296797361-0.03694974902530.421362825344-0.4699527777320.271309077102-0.3754171120410.312524099690.0295469888755-0.03490370580360.484812575641-0.0219834778210.49064370747725.0959202399-25.156328314810.842466009
676.10560924731.05545405405-3.133264707233.95523054504-4.88989787186.619120141370.01419032469290.514066075802-0.093300585542-1.191796653920.1061699189721.176007713291.96676993146-1.63728005253-0.3171754685390.756220946777-0.118001248118-0.2297656702750.841405061052-0.1863187542161.113687129256.72056835975-51.73340361798.86831529166
683.98161005552-2.383541264781.85827847486.317643138442.850823530064.17304275218-0.1149547728480.253317080372-1.01938117361-0.422384599102-0.6737440863380.3844767057650.9203276685010.07677372956230.519796989480.4363775377190.00686453670779-0.1957976367590.5190254511490.143295488550.66566964160216.3237409997-56.7342394966-20.8237530567
695.81184576065-3.07388933942-1.798821449564.83132577353.495957850325.204054212470.6244734360320.422034090369-1.01737994071-0.498298303727-0.4558310287390.8493147487160.39867946051-0.301456864852-0.05125829423010.5360522093150.0720996794051-0.2043890361170.3981059657760.02157869694550.69644719542514.6643782492-50.2473109576-12.1894701304
701.44038887078-1.3263575496-0.1935158933053.948616406731.308714573944.03380916698-0.1096682821480.2205965199860.531301683543-0.3220753651690.1469390096010.376965537225-0.27478483094-0.223200582851-0.0653336608550.451772779131-0.0385856847691-0.1594877441290.4242861109870.06130080427880.49039242021220.0652597212-45.9211421798-15.9607535843
710.300473100628-0.8655262332320.06742210476213.137269677731.368032994784.51104212453-0.0549372634029-0.18820578651-0.102166691709-0.1698485666540.110130991922-0.0224648434540.1568012679650.249770833029-0.0926865398470.417189211234-0.0232445967313-0.2184582850750.405500090815-0.09065198834920.65068548050421.9760784377-49.6361950772-12.3115320864
722.64468219843-2.043898654020.2166523656446.809339915981.847496242030.779227857550.4166801391850.495592644951-0.626938896653-0.521967647158-0.4025853815320.7780108049640.190842133068-0.05754712316560.00978233846280.5918357820730.0487214702164-0.2820965569940.579739937714-0.06261185746560.74745562304723.0944691412-75.1542899821-21.9894351763
733.447026439780.699254692665-0.7685296969092.468843716540.3087846790076.195360406330.3874238456920.188432948027-0.8637942802860.379205802394-0.522958919212-0.0100307201758-0.865055446711-0.796188200291-0.1152398645520.6965862168670.182422604629-0.3215002119830.532024739174-0.1563280453290.83892576135922.7913497123-78.7618072682-19.2566720402
743.17298514480.00795535593086-0.3893726234431.137472590061.912122763785.881001962450.518728209215-0.0280837482292-1.661691453140.0828007040835-0.393377699598-0.32579662491.20694722869-0.6067365662840.09315919682311.09834094139-0.0852194013597-0.5468450950890.626478596723-0.003134599778311.1073875741224.5111953749-89.4483407226-16.860891933
752.59757941175-1.30415035505-0.6211843873646.11400787745-0.5062690190184.524764548450.634811882231-0.133949687696-1.13325402629-1.12076329214-0.382399144432.054119497690.681730193551-1.07694401349-0.328016199160.739272085118-0.0673266020656-0.4765274427070.9600645191610.01118104507451.2885648416815.4824778573-84.8008395586-21.4952126989
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 'C' and (resid 212 through 222 )CS212 - 222208 - 218
22chain 'E' and (resid 1 through 8 )ET1 - 81 - 8
33chain 'E' and (resid 9 through 25 )ET9 - 259 - 25
44chain 'E' and (resid 26 through 41 )ET26 - 4126 - 41
55chain 'E' and (resid 42 through 74 )ET42 - 7442 - 74
66chain 'E' and (resid 75 through 84 )ET75 - 8475 - 84
77chain 'E' and (resid 85 through 101 )ET85 - 10185 - 101
88chain 'E' and (resid 102 through 111 )ET102 - 111102 - 111
99chain 'E' and (resid 112 through 128 )ET112 - 128112 - 128
1010chain 'F' and (resid 1 through 8 )FAA - F1 - 81 - 8
1111chain 'F' and (resid 9 through 16 )FF9 - 169 - 16
1212chain 'F' and (resid 17 through 39 )FF17 - 3917 - 41
1313chain 'F' and (resid 40 through 70 )FF40 - 7042 - 72
1414chain 'F' and (resid 71 through 85 )FF71 - 8573 - 87
1515chain 'F' and (resid 86 through 101 )FF86 - 10188 - 103
1616chain 'F' and (resid 102 through 113 )FF102 - 113104 - 115
1717chain 'D' and (resid 1 through 18 )DD1 - 181 - 18
1818chain 'D' and (resid 19 through 38 )DD19 - 3819 - 38
1919chain 'D' and (resid 39 through 75 )DD39 - 7539 - 75
2020chain 'D' and (resid 76 through 90 )DD76 - 9076 - 90
2121chain 'D' and (resid 91 through 102 )DD91 - 10291 - 102
2222chain 'D' and (resid 103 through 113 )DD103 - 113103 - 113
2323chain 'D' and (resid 114 through 150 )DD114 - 150114 - 150
2424chain 'D' and (resid 151 through 163 )DD151 - 163151 - 165
2525chain 'D' and (resid 164 through 213 )DD164 - 213166 - 217
2626chain 'R' and (resid 334 through 358 )RA334 - 3581 - 25
2727chain 'R' and (resid 359 through 380 )RA359 - 38026 - 47
2828chain 'R' and (resid 381 through 393 )RA381 - 39348 - 60
2929chain 'R' and (resid 394 through 451 )RA394 - 45161 - 118
3030chain 'R' and (resid 452 through 494 )RA452 - 494119 - 161
3131chain 'R' and (resid 495 through 516 )RA495 - 516162 - 183
3232chain 'R' and (resid 517 through 527 )RA517 - 527184 - 194
3333chain 'A' and (resid 1 through 17 )AE1 - 171 - 17
3434chain 'A' and (resid 18 through 83 )AE18 - 8318 - 83
3535chain 'A' and (resid 84 through 98 )AE84 - 9884 - 98
3636chain 'A' and (resid 99 through 153 )AE99 - 15399 - 147
3737chain 'A' and (resid 154 through 183 )AE154 - 183148 - 177
3838chain 'A' and (resid 184 through 211 )AE184 - 211178 - 205
3939chain 'A' and (resid 212 through 222 )AE212 - 222206 - 216
4040chain 'H' and (resid 1 through 8 )HF1 - 81 - 8
4141chain 'H' and (resid 9 through 33 )HF9 - 339 - 33
4242chain 'H' and (resid 34 through 62 )HF34 - 6234 - 62
4343chain 'H' and (resid 63 through 74 )HF63 - 7463 - 74
4444chain 'H' and (resid 75 through 84 )HF75 - 8475 - 84
4545chain 'H' and (resid 85 through 101 )HF85 - 10185 - 101
4646chain 'H' and (resid 102 through 111 )HF102 - 111102 - 111
4747chain 'H' and (resid 112 through 128 )HF112 - 128112 - 128
4848chain 'L' and (resid 1 through 8 )LM1 - 81 - 8
4949chain 'L' and (resid 9 through 23 )LM9 - 239 - 25
5050chain 'L' and (resid 24 through 70 )LM24 - 7026 - 72
5151chain 'L' and (resid 71 through 85 )LM71 - 8573 - 87
5252chain 'L' and (resid 86 through 101 )LM86 - 10188 - 103
5353chain 'L' and (resid 102 through 113 )LM102 - 113104 - 115
5454chain 'B' and (resid 1 through 18 )BN1 - 181 - 18
5555chain 'B' and (resid 19 through 61 )BN19 - 6119 - 61
5656chain 'B' and (resid 62 through 102 )BN62 - 10262 - 102
5757chain 'B' and (resid 103 through 113 )BN103 - 113103 - 113
5858chain 'B' and (resid 114 through 128 )BN114 - 128114 - 128
5959chain 'B' and (resid 129 through 150 )BN129 - 150129 - 150
6060chain 'B' and (resid 151 through 163 )BN151 - 163151 - 165
6161chain 'B' and (resid 164 through 198 )BN164 - 198166 - 202
6262chain 'B' and (resid 199 through 213 )BN199 - 213203 - 217
6363chain 'X' and (resid 334 through 358 )XO334 - 3581 - 25
6464chain 'X' and (resid 359 through 421 )XO359 - 42126 - 88
6565chain 'X' and (resid 422 through 487 )XO422 - 48789 - 154
6666chain 'X' and (resid 488 through 516 )XO488 - 516155 - 183
6767chain 'X' and (resid 517 through 527 )XO517 - 527184 - 194
6868chain 'C' and (resid 1 through 17 )CS1 - 171 - 17
6969chain 'C' and (resid 18 through 40 )CS18 - 4018 - 40
7070chain 'C' and (resid 41 through 83 )CS41 - 8341 - 83
7171chain 'C' and (resid 84 through 108 )CS84 - 10884 - 108
7272chain 'C' and (resid 109 through 153 )CS109 - 153109 - 147
7373chain 'C' and (resid 154 through 183 )CS154 - 183148 - 177
7474chain 'C' and (resid 184 through 198 )CS184 - 198178 - 194
7575chain 'C' and (resid 199 through 211 )CS199 - 211195 - 207

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る