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- PDB-7ps4: Crystal structure of the receptor binding domain of SARS-CoV-2 be... -

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基本情報

登録情報
データベース: PDB / ID: 7ps4
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-38
要素
  • Beta-38 Fab heavy chain
  • Beta-38 Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-COV-2 B.1.1.7 (Alpha) VARIANT / B.1.351 (Beta) VARIANT / P.1 (Gamma) VARIANT / B.1.617.2 (Delta) VARIANT / ANTIBODY / RECEPTOR-BINDING-DOMAIN / SPIKE / NEUTRALISATION / VIRAL PROTEIN/IMMUNE SYSTEM / 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 / 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 / symbiont-mediated suppression of host innate immune response / 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
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: 1.94 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
Medical Research Council (MRC, United Kingdom)MR/ N00065X/1 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 英国
引用ジャーナル: Cell Host Microbe / 年: 2022
タイトル: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
著者: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James ...著者: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James Brett Case / Yuguang Zhao / Donal T Skelly / Rita E Chen / Sile Ann Johnson / Thomas G Ritter / Chris Mason / Tariq Malik / Nigel Temperton / Neil G Paterson / Mark A Williams / David R Hall / Daniel K Clare / Andrew Howe / Philip J R Goulder / Elizabeth E Fry / Michael S Diamond / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape ...Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
履歴
登録2021年9月22日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年12月15日Provider: repository / タイプ: Initial release
改定 1.12021年12月22日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
改定 1.22021年12月29日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.32022年1月26日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
改定 1.42024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
H: Beta-38 Fab heavy chain
L: Beta-38 Fab light chain
A: Spike protein S1
B: Beta-38 Fab heavy chain
C: Beta-38 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)142,82610
ポリマ－141,9066
非ポリマー9204
水8,467470
1
E: Spike protein S1
H: Beta-38 Fab heavy chain
L: Beta-38 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,4135
ポリマ－70,9533
非ポリマー4602
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Spike protein S1
B: Beta-38 Fab heavy chain
C: Beta-38 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,4135
ポリマ－70,9533
非ポリマー4602
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)55.071, 118.487, 109.268
Angle α, β, γ (deg.)90.000, 93.466, 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 333 through 365 or resid 367...
d_2ens_1(chain "E" and (resid 333 through 365 or resid 367...
d_1ens_2(chain "B" and (resid 1 through 108 or resid 110...
d_2ens_2(chain "H" and (resid 1 through 108 or resid 110...
d_1ens_3(chain "C" and (resid 2 through 8 or resid 10...
d_2ens_3(chain "L" and (resid 2 through 8 or resid 10...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRTYRD1 - 33
d_12ens_1VALLEUD35 - 36
d_13ens_1ASNILED38 - 70
d_14ens_1GLYGLYD72 - 84
d_15ens_1ILEGLYD86 - 153
d_16ens_1ASNGLYD155 - 194
d_21ens_1THRTYRA1 - 33
d_22ens_1VALLEUA35 - 36
d_23ens_1ASNILEA38 - 70
d_24ens_1GLYGLYA72 - 84
d_25ens_1ILEGLYA86 - 153
d_26ens_1ASNGLYA155 - 194
d_11ens_2GLUTYRE1 - 108
d_12ens_2TYRLYSE110 - 141
d_13ens_2GLYHISE146 - 212
d_14ens_2PROSERE214 - 215
d_15ens_2THRLYSE217 - 226
d_21ens_2GLUTYRB1 - 108
d_22ens_2TYRHISB110 - 208
d_23ens_2PROSERB210 - 211
d_24ens_2THRLYSB213 - 222
d_11ens_3SERPROF1 - 7
d_12ens_3ALATHRF9 - 104
d_13ens_3VALPROF106 - 112
d_14ens_3ALAPROF114 - 211
d_21ens_3SERPROC2 - 8
d_22ens_3ALATHRC10 - 105
d_23ens_3VALPROC107 - 113
d_24ens_3ALAPROC115 - 212

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.876255658943, -0.471322948625, -0.100153373738), (-0.462723199612, 0.765125647623, 0.447738745129), (-0.134399630625, 0.438676898695, -0.88853774137)53.1258402168, 0.283152838535, 53.849491743
2given(-0.770354651693, -0.636836749212, 0.0315065940433), (-0.623544869894, 0.762757857166, 0.171441671015), (-0.133212258607, 0.112425113677, -0.984690351314)51.9318592659, 8.29380681731, 58.4358022918
3given(-0.787241892051, -0.612789100875, -0.0688456334757), (-0.616615020827, 0.781194843595, 0.0975732157452), (-0.00600994927075, 0.119264974696, -0.992844270931)53.3138280077, 8.0941498406, 56.5544568015

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要素

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抗体 , 2種, 4分子 HBLC

#2: 抗体 Beta-38 Fab heavy chain


分子量: 24599.629 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 Beta-38 Fab light chain


分子量: 22706.934 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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タンパク質 / 糖 , 2種, 4分子 EA

#1: タンパク質 Spike protein S1


分子量: 23646.551 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
#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 合成
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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非ポリマー , 2種, 472分子

#5: 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: 天然 / 式: Cl
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 470 / 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

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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: 2.6 Å3/Da / 溶媒含有率: 52.71 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.8 M Sodium/potassium phosphate pH 7.5

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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: 0.97623 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2021年8月11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: 0.97623 Å / 相対比: 1
反射解像度: 1.94→59 Å / Num. obs: 101364 / % possible obs: 98 % / 冗長度: 6.2 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.029 / Net I/σ(I): 17.1
反射 シェル解像度: 1.94→1.97 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4165 / CC1/2: 0.321

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解析

ソフトウェア
名称バージョン分類
GDA1.19_4092データ収集
PHENIX1.19_4092精密化
xia2データ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6YLA

6yla


解像度: 1.94→54.53 Å / SU ML: 0.2918 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.976
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2312 5034 4.99 %
Rwork0.2035 95822 -
obs0.2049 100856 97.52 %
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: 66.22 Å2
精密化ステップサイクル: LAST / 解像度: 1.94→54.53 Å
タンパク質核酸リガンド溶媒全体
原子数9604 0 58 470 10132
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00449939
X-RAY DIFFRACTIONf_angle_d0.733313564
X-RAY DIFFRACTIONf_chiral_restr0.05011503
X-RAY DIFFRACTIONf_plane_restr0.00561744
X-RAY DIFFRACTIONf_dihedral_angle_d11.85523520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS0.869540622914
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS1.59293902754
ens_3d_2FX-RAY DIFFRACTIONTorsion NCS1.91129360259
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.34781280.36162372X-RAY DIFFRACTION72.28
1.96-1.980.3661240.33772621X-RAY DIFFRACTION79.45
1.98-2.010.30761460.32922827X-RAY DIFFRACTION87.16
2.01-2.030.35431420.31943066X-RAY DIFFRACTION92.64
2.03-2.060.33881670.32693098X-RAY DIFFRACTION96.14
2.06-2.090.34031550.31343226X-RAY DIFFRACTION99
2.09-2.120.3351810.29163307X-RAY DIFFRACTION99.97
2.12-2.150.32241750.27463235X-RAY DIFFRACTION99.94
2.15-2.180.30251610.26773288X-RAY DIFFRACTION99.97
2.18-2.220.31091700.26673264X-RAY DIFFRACTION99.97
2.22-2.260.28511770.25883223X-RAY DIFFRACTION99.85
2.26-2.30.27182170.25013245X-RAY DIFFRACTION99.91
2.3-2.340.28051640.23223229X-RAY DIFFRACTION99.91
2.34-2.390.24911670.23373314X-RAY DIFFRACTION99.94
2.39-2.440.27921840.23823224X-RAY DIFFRACTION100
2.44-2.50.26931850.23763283X-RAY DIFFRACTION99.97
2.5-2.560.29391720.24763248X-RAY DIFFRACTION100
2.56-2.630.3021680.25113284X-RAY DIFFRACTION100
2.63-2.710.2811890.25263244X-RAY DIFFRACTION99.97
2.71-2.80.28531630.23893291X-RAY DIFFRACTION99.97
2.8-2.90.28151640.23083306X-RAY DIFFRACTION99.97
2.9-3.010.27821550.22913250X-RAY DIFFRACTION100
3.01-3.150.24111810.22993274X-RAY DIFFRACTION100
3.15-3.320.24541710.22553289X-RAY DIFFRACTION99.97
3.32-3.520.23931790.20883281X-RAY DIFFRACTION100
3.52-3.80.22811870.1933245X-RAY DIFFRACTION100
3.8-4.180.19191640.16883313X-RAY DIFFRACTION100
4.18-4.780.14241440.13813314X-RAY DIFFRACTION100
4.78-6.020.1781920.14883304X-RAY DIFFRACTION100
6.02-54.530.18541620.17083357X-RAY DIFFRACTION99.77
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)
12.128391076450.6111275653430.5804048048428.93262784746-2.897195098492.19742056121-0.228910183873-1.17515604566-1.060950487871.504574932570.1797336471950.9073319749111.06509930778-0.123055602098-0.002151965706380.9861881788260.07481393921040.212323690670.6751727297410.1586520300440.72163572196412.2723762378-23.014672371440.7119640557
27.47307233097-3.44090305869-0.8838785289876.85456056942-1.225265878961.43344794453-0.346408990768-0.918099439693-1.604918600820.06107539480080.16586151071.430002079281.57794239193-0.5554044027470.474801674421.16237497599-0.1973098661190.1823555437190.654608878722-0.03098906027891.046824391619.41686271377-33.045808162129.4916654923
35.438108904790.228238725947-0.4842092226153.470445447921.589413995833.87197172668-0.375980618367-0.0159908043911-0.3763350459520.220803240170.03389524081390.1856359201010.5288306796270.01512791935890.1933135056010.3189394981450.002268652430370.01774573610930.2772335578470.02877827935070.33129451816818.6126941217-14.676235820430.8701143743
46.644829032070.597744585737-0.4643146908764.649261697462.615606468114.142053770290.0936040593508-0.105061770660.127509219956-0.7463204899030.138512518942-0.647485530027-0.7648814611290.405849582463-0.2830415704650.4212172225410.000312913526906-0.03046081990320.318358989259-0.07568311695930.37686623100830.47043892093.2475495955334.3884222422
53.501307975930.911447928383-0.03735791447082.768319970741.429689516913.82841485838-0.29076965892-0.164992797485-0.7949180073650.634786401595-0.06310394580110.2292987081620.8011164612940.05107650872520.2519973096410.51442655362-0.04266393595270.1529703059780.4275713357240.03523554044570.52983581552112.7976098214-20.659241231.9020606568
62.84151943525-0.105366908656-0.3661577613758.33259614844-1.49160848653.078794675910.240188134994-0.1536595073960.4671535064750.88831100931-0.130541837283-0.366415733955-0.9757329331450.357481707364-0.008877755061080.392295185798-0.0884481439196-0.08470101580970.33325698917-0.07806021633090.51426164703932.760893567631.829274543749.6817469833
72.06229803176-0.0762629513390.2642427568575.71937559294-0.2874167622382.299443501370.09560900212010.09093246437240.0817399803824-0.000924403036060.00496043462123-0.558132169267-0.136609145770.122501271722-0.03635220927240.27578873898-0.04591497336410.006870111400670.297777791196-0.01815206871520.40857214799231.639711230920.071910037444.9850129096
83.920824812910.4354200305790.9071650726994.791964684350.02103183997672.379334435570.04356781685720.5145218299260.411630430544-0.348605425975-0.118689185551-0.910266147519-0.01572189184380.361118311797-0.03305876386630.319091841518-0.04448769797240.08832433516170.3255032223890.005299513418320.48530944792734.592454629723.05243056539.0505312941
93.88177318816-1.443970037450.08729324248327.67212235775-1.110237191052.202762964930.552332642170.2349522197570.314999562918-0.302797826234-0.260788932134-0.568349532197-0.06747288683550.3489215052330.01315853506480.371409760742-0.04758847843340.02371370934940.3286944499740.0008268684355010.4503596219532.840198274730.825809588841.7307658259
100.795642035738-1.045959290790.0163167553166.39356556495-0.2545878969170.1353256261530.03518640139680.02059003470110.1742497096050.0949697957871-0.0548376337149-0.55138369349-0.090202947943-0.0272545559009-0.01122954277150.341395198197-0.0317092584353-0.004835817213610.338985737097-0.01984598034120.38060227707425.223751509222.843800103547.5601763366
111.67712823616-0.259797741519-0.9875898959084.93702350858-0.2490188523533.21777651347-0.1869425391860.571482291594-0.3076340370290.142352913295-0.0775422575520.958532890870.148914143823-1.102370745210.2022860968040.339047434279-0.066038719039-0.01751539547490.481558191134-0.1203859948870.645328568241.2906148631854.768491873149.7168535312
123.04025725424-2.14732889436-2.680296969163.677300970931.554824008022.662134119340.172922691279-0.453805103570.1397919181580.156091824446-0.077189035689-0.109915167170.1620128570260.2245971924960.2188804712210.376625605163-0.0431982560893-0.1033153794610.383173076414-0.003712328208780.52806136448312.097432765454.008743626156.7717429274
133.5232609721-0.913560309812-1.173019086444.750418888321.406991511824.54309206792-0.08192739009570.0136820906818-0.1020142856970.3559988314-0.1319018193730.4461536940850.0219427732915-0.48354626020.2806335728670.282520658319-0.0107709406169-0.02454108990180.312246580579-0.04105377822610.4603888444525.2612144226553.253526044455.2111141073
141.98717990833-1.11742491287-2.283501322916.763405707811.061462377635.24871391749-0.04634779432660.266285744261.02730827014-0.661414556904-0.3082288753070.317854558213-0.539357311087-0.6634795296420.1041768976860.4878459880920.117089367946-0.1337114159150.383927969643-0.07949470121160.6730151958984.7883939598462.882111736152.5159739358
150.498045545969-0.9057502788630.344272437534.790845421181.791795090737.07174223180.2478872414160.3730293778130.08479818750240.2207337655270.03000658663031.25712381539-0.30175806674-1.14065152165-0.1868037263750.2524393432720.03785363264950.04609324201290.4569443548850.03330481489640.7350951272654.9915577707216.303374412550.1547243075
162.93246527103-0.368706034438-0.8825844464365.18033576889-0.7030902331120.8897702618410.109270652522-0.0618298415890.03041296826110.4550195108180.03936940303410.735280871413-0.114312633185-0.137925613447-0.004706073044770.276846189318-0.04314784043490.02379674275350.302665069164-0.001255756989370.4351780150812.757733857414.652686442151.52580975
176.955824450942.18768092619-3.460794608373.2514434537-3.081387464063.562976992740.03910961163080.2809427404250.0850973838528-0.418867434391-0.7127149543320.533675475738-0.51121376923-0.4392524945550.4184000981090.7232251988340.0268385176931-0.1977065536020.574298774031-0.1054289367310.7470797829370.27278984670754.812850581442.6006723648
182.52619225343-0.540770716848-1.36133237125.9918265193-0.06862432264235.32820049823-0.2055394763670.439657950248-0.361761700638-0.6753276218-0.06879809249991.230070737960.753863043857-0.779233779390.1585479461430.469042897397-0.141046356742-0.06572004226270.4595661203-0.1399038063820.706394406859-1.246621622241.5740992244.1206336969
199.45316980314-2.97991076663-6.391818128737.154630222154.635818993938.824596812970.351369989910.5152590804290.11085239442-1.08129698792-0.0877263603485-0.411074667726-0.8948305523160.306573354889-0.3881166083260.48682504727-0.070870725207-0.0207504887750.6185457188640.05313595668750.27041370722748.4564461212-4.420131792515.39048278778
200.6507323085620.133115974157-0.8303759506781.803993242421.812968304564.02275905265-0.170795873785-0.00717521177062-0.30587720431-0.08891722640280.590914581718-0.7781056914320.3271911837221.44128200435-0.3078774151330.4053647074990.126890293849-0.02163066454971.03642245743-0.1186104302570.70698623725456.7179169985-15.500072506610.6437848592
214.43929183876-1.45465893404-1.006934583523.13314642824-0.09436104340631.42215298036-0.0249026022631-0.04765598093970.1530306181650.1323196402960.102482096607-0.160440187053-0.2584882019490.205576305807-0.07412562174710.271761828061-0.0429192658742-0.04729967491120.379328497819-0.0177169843390.24223504969137.9096049525-2.5474987570618.4291888623
228.999620351567.734949254090.1953623308298.084032737791.890391737192.08921372503-0.00479213363233-0.575257871173-0.216850485864-0.57773067843-0.0995964804628-1.10489708970.515245273530.1928811722560.02636840899740.6957571256820.0314776496709-0.08960451910860.572051582839-0.08186820575210.5769243460650.0744250211-22.602573117-0.700954706844
233.00238089567-1.431891130220.07750508005814.47548959523-0.2864287029982.64984693953-0.0160957695495-0.35053378836-0.0572829241398-0.1112661583190.02312431212220.286510637426-0.213114369582-0.2901212028510.05307575416580.4411637555270.00881821834167-0.0106575879890.4798252958320.118019158810.3964119531889.4047254596222.926595385314.7763354137
241.81295736180.348442570408-1.297321719495.87279189751-3.097049975622.153051679430.3344201552560.8520192447930.10219140517-2.67447213271-0.152568645811.178169982980.465638963256-0.191223051203-0.1097731745912.274090074750.285208182156-0.2714617581290.858696465482-0.05875342380410.9841033038257.3646508502264.170620230911.4669224404
252.751060170530.590732820581-0.483263609776.70981437447-0.6836344757953.313033108140.196102447292-0.06929470451150.339068979851-0.636355758403-0.324112903452-1.01079236008-0.6645124991010.5943334719930.154683267170.596604682513-0.08544859877940.1057912644160.5088710785310.106477743090.52490200079529.031239594929.45132728548.70679116559
263.34704663529-1.05574789775-1.617512896936.214610173521.760611278172.700900349230.176132808795-0.03824743508020.145135733701-0.434081666838-0.10825295314-0.0567254271717-0.0234289172198-0.0192793816626-0.002450607592211.5483360291-0.0009157502356750.1484438078010.572431734089-0.0002671272986230.76197567782220.659553954661.113008772219.9413082703
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 358 )EA333 - 3581 - 26
22chain 'E' and (resid 359 through 393 )EA359 - 39327 - 61
33chain 'E' and (resid 394 through 469 )EA394 - 46962 - 137
44chain 'E' and (resid 470 through 494 )EA470 - 494138 - 162
55chain 'E' and (resid 495 through 526 )EA495 - 526163 - 194
66chain 'H' and (resid 1 through 17 )HB1 - 171 - 17
77chain 'H' and (resid 18 through 60 )HB18 - 6018 - 60
88chain 'H' and (resid 61 through 76 )HB61 - 7661 - 76
99chain 'H' and (resid 77 through 91 )HB77 - 9177 - 91
1010chain 'H' and (resid 92 through 131 )HB92 - 13192 - 131
1111chain 'H' and (resid 132 through 157 )HB132 - 157132 - 153
1212chain 'H' and (resid 158 through 169 )HB158 - 169154 - 165
1313chain 'H' and (resid 170 through 215 )HB170 - 215166 - 211
1414chain 'H' and (resid 216 through 227 )HB216 - 227212 - 223
1515chain 'L' and (resid 1 through 23 )LC1 - 231 - 23
1616chain 'L' and (resid 24 through 117 )LC24 - 11724 - 117
1717chain 'L' and (resid 118 through 133 )LC118 - 133118 - 133
1818chain 'L' and (resid 134 through 213 )LC134 - 213134 - 213
1919chain 'A' and (resid 333 through 358 )AD333 - 3581 - 26
2020chain 'A' and (resid 359 through 393 )AD359 - 39327 - 61
2121chain 'A' and (resid 394 through 516 )AD394 - 51662 - 184
2222chain 'A' and (resid 517 through 527 )AD517 - 527185 - 195
2323chain 'B' and (resid 1 through 123 )BE1 - 1231 - 123
2424chain 'B' and (resid 124 through 228 )BE124 - 228124 - 228
2525chain 'C' and (resid 2 through 117 )CF2 - 1171 - 116
2626chain 'C' and (resid 118 through 214 )CF118 - 214117 - 213

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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://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