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- PDB-7pry: 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: 7pry
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with COVOX-45 and beta-6 Fabs
要素
  • (COVOX-45 Fab ...) x 2
  • Beta-6 Fab heavy chain
  • Beta-6 Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 alpha variant / beta variant / gamma variant / delta variant / B.1.1.7 / B.1.351 / P.1 / B.1.617.2 / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM
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
Spike glycoprotein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 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
A: COVOX-45 Fab heavy chain
B: COVOX-45 Fab light chain
H: Beta-6 Fab heavy chain
L: Beta-6 Fab light chain
E: Spike protein S1
F: COVOX-45 Fab heavy chain
G: COVOX-45 Fab light chain
C: Beta-6 Fab heavy chain
D: Beta-6 Fab light chain
I: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)239,58712
ポリマ－238,44610
非ポリマー1,1412
水00
1
A: COVOX-45 Fab heavy chain
B: COVOX-45 Fab light chain
C: Beta-6 Fab heavy chain
D: Beta-6 Fab light chain
I: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,7946
ポリマ－119,2235
非ポリマー5711
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
H: Beta-6 Fab heavy chain
L: Beta-6 Fab light chain
E: Spike protein S1
F: COVOX-45 Fab heavy chain
G: COVOX-45 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,7946
ポリマ－119,2235
非ポリマー5711
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)86.393, 166.778, 120.180
Angle α, β, γ (deg.)90.000, 108.518, 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_1chain "A"
d_2ens_1chain "F"
d_1ens_2(chain "B" and (resid 1 through 80 or resid 82 through 213))
d_2ens_2(chain "G" and (resid 1 through 80 or resid 82 through 213))
d_1ens_3(chain "C" and resid 2 through 224)
d_2ens_3chain "H"
d_1ens_4chain "D"
d_2ens_4chain "L"
d_1ens_5chain "E"
d_2ens_5chain "I"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSA1 - 216
d_21ens_1GLNLYSI1 - 216
d_11ens_2ASPPROB1 - 80
d_12ens_2ASPGLUB82 - 213
d_21ens_2ASPPROJ1 - 80
d_22ens_2ASPGLUJ82 - 213
d_11ens_3VALLYSK1 - 218
d_21ens_3VALLYSC1 - 218
d_11ens_4GLUCYSL1 - 215
d_21ens_4GLUCYSD1 - 215
d_11ens_5ASNGLYE1 - 193
d_12ens_5FUCFUCF
d_13ens_5NAGNAGG
d_14ens_5NAGNAGH
d_21ens_5ASNGLYJ1 - 193
d_22ens_5FUCFUCL
d_23ens_5NAGNAGL
d_24ens_5NAGNAGL

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(0.715340807895, 0.0684439049559, -0.695415674567), (0.0748937275401, -0.996968610446, -0.0210836278053), (-0.694750644573, -0.0370002927106, -0.718298350412)-61.9329359318, 82.5920952983, -140.094472403
2given(0.731897041013, 0.0612200881263, -0.678659577525), (0.0716932471251, -0.997346497652, -0.0126507682667), (-0.67763323389, -0.0393962489443, -0.734344017403)-60.7501438715, 83.6543351684, -140.768978033
3given(0.697353933316, 0.011573344497, -0.716633483299), (0.00448911347762, -0.999920536878, -0.0117799741415), (-0.716712871064, 0.00499776227352, -0.697350473452)-58.4765453788, 84.031694907, -141.320471428
4given(0.70069498508, 0.0271522189445, -0.712944103622), (0.00800441221764, -0.999511850913, -0.0301991600811), (-0.713416054816, 0.015453701529, -0.700570279016)-59.6162041854, 83.8732535508, -142.162718672
5given(0.71756787787, 0.0279959959421, -0.69592568918), (0.0332432692421, -0.999429706928, -0.00592840287433), (-0.695694779124, -0.0188808135882, -0.718089332311)-57.633588624, 84.3011187666, -141.94107108

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要素

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抗体 , 4種, 8分子 AFBGHCLD

#1: 抗体 COVOX-45 Fab 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)
#2: 抗体 COVOX-45 Fab light chain


分子量: 23359.775 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-6 Fab heavy chain


分子量: 24377.293 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 Beta-6 Fab light chain


分子量: 23652.232 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 EI

#5: 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
#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: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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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: 3.56 Å3/Da / 溶媒含有率: 65.47 %
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: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, and 18% (w/v) PEG 20000

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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: 2021年7月28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: 3.1→74 Å / Num. obs: 58580 / % possible obs: 100 % / 冗長度: 6.4 % / Biso Wilson estimate: 89.11 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.106 / Net I/σ(I): 6.6
反射 シェル解像度: 3.1→3.15 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2879 / CC1/2: 0.34

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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: 7BEL

7bel


解像度: 3.1→58.32 Å / SU ML: 0.5805 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 34.8322
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2909 2711 4.64 %
Rwork0.2445 55715 -
obs0.2467 58426 99.7 %
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: 106.89 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→58.32 Å
タンパク質核酸リガンド溶媒全体
原子数16222 0 76 0 16298
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002716700
X-RAY DIFFRACTIONf_angle_d0.546122748
X-RAY DIFFRACTIONf_chiral_restr0.04172554
X-RAY DIFFRACTIONf_plane_restr0.00492906
X-RAY DIFFRACTIONf_dihedral_angle_d11.9785960
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.654317581196
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.586909671409
ens_3d_2KX-RAY DIFFRACTIONTorsion NCS0.52040367679
ens_4d_2LX-RAY DIFFRACTIONTorsion NCS0.462450622136
ens_5d_2EX-RAY DIFFRACTIONTorsion NCS0.091468240218
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.44611170.38412874X-RAY DIFFRACTION96.98
3.16-3.220.40131330.3632904X-RAY DIFFRACTION99.61
3.22-3.280.37021270.33862963X-RAY DIFFRACTION99.84
3.28-3.350.34831230.31042947X-RAY DIFFRACTION99.84
3.35-3.430.31751260.30312955X-RAY DIFFRACTION99.9
3.43-3.520.32091530.29152886X-RAY DIFFRACTION99.9
3.52-3.610.31421340.27392948X-RAY DIFFRACTION99.97
3.61-3.720.3311440.27132895X-RAY DIFFRACTION99.8
3.72-3.840.30871550.26882944X-RAY DIFFRACTION99.94
3.84-3.970.34761450.2572916X-RAY DIFFRACTION99.8
3.97-4.130.32891420.24422968X-RAY DIFFRACTION99.9
4.13-4.320.26111750.21842892X-RAY DIFFRACTION99.97
4.32-4.550.2551270.21172959X-RAY DIFFRACTION99.87
4.55-4.830.241320.21222937X-RAY DIFFRACTION100
4.83-5.210.29851540.21262928X-RAY DIFFRACTION99.94
5.21-5.730.28061570.21732950X-RAY DIFFRACTION99.97
5.73-6.560.27411610.23612909X-RAY DIFFRACTION99.97
6.56-8.260.26641460.23812967X-RAY DIFFRACTION99.97
8.26-58.320.25591600.21632973X-RAY DIFFRACTION99.27
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)
12.58353125724-1.738907598071.372527132327.222665403241.781470017875.114885465490.01390927330440.08659550819540.0926018633116-0.429089625804-0.3448640758290.37266670125-0.335597534431-0.1790970048920.2891820098940.4317172444470.00373834480924-0.1358797925120.5892601773260.02620397487850.7110431550274.2787320119646.0362269016-63.445983224
21.184096255430.937403860247-0.9571806127911.7812746369-0.306385371330.781646996102-0.1578277389620.30346503268-0.739996588929-0.2123341863980.1480677936560.160200324580.297022348317-0.6168579958080.0215374255130.528007121202-0.044754486648-0.1827226512090.9403365989840.02892352664361.15276282458-16.133858422717.4893548917-66.4220989177
32.265859575522.07866157517-0.5280703808555.00812898641-0.8226241764263.28330221308-0.04010227225550.0381459058568-0.01917771300340.843114836095-0.2893999690871.02726228720.205936877661-0.2756071401810.1917636240590.512066280431-0.04424589068420.1269173481180.552558909926-0.03831423897230.820829146549-8.8692490887544.7986552881-42.7284102702
46.077455564440.160475936516-2.995045494215.657966825932.209608792263.23020385683-0.3913303610631.369033979880.30820747546-1.65076601211-1.492921156742.19111513518-0.590198157179-1.911243292320.066172958223-0.0247610639476-0.7891627169860.0784188649326-0.2345136347060.2728721536911.25698972126-14.813439694541.1448877032-46.159922317
51.294575855542.296935949190.793041471564.221016120780.2375397653760.9730744159840.3778134624890.05664495082310.002007307722950.196777494252-0.1854121424610.009535938577330.437125460348-0.0374243650734-0.1302063978820.5229057753830.0917054279257-0.08630251782920.760533022294-0.05115613261290.990079796814-10.778640963822.6665553811-51.9027081614
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532.31031539363-0.5893250032281.105504021790.167684071738-0.3640893289650.742333529854-0.272827556873-0.942375659029-1.823685646220.2098687648120.54822818038-0.4041721631531.98789800489-0.210484575997-0.2075423523971.969548816280.4015280982-0.3728253453661.11296574583-0.2297671211451.476860180665.13120937451.80410792253.98256481898
545.266131198460.800997595651-0.4546889062371.83450473609-3.387464122969.61485990195-0.2421143473550.0887718116121-0.817879687529-0.0384839556779-0.0650379956841-0.5362191898771.345498883660.8721253728790.3632038482721.224342199150.134758123595-0.2786313605680.807882445377-0.09892662394481.205416701763.937217207760.71962978643.96096363019
552.3766071134-1.86136863609-0.8772717556432.438949373151.796335886625.77297833205-0.804563025964-1.05399536295-0.1778519520310.5035276481210.7438352686810.06092072732460.4339084714650.09815263264520.126574626290.640588671363-0.06658986651930.04227593457970.5520240504990.2171058101610.793552659522-0.53097136633463.5641373558-39.79100216
563.35685560551.055398208714.015235921351.52371426663-0.4458838662616.94633055304-0.507978553901-1.161871946850.245646027770.53493802449-0.586679800521.59259208478-1.74835989048-1.971055034050.1901149587130.236079982961-0.00766585700520.2435353133321.10225940337-0.3632227849131.43463978972-7.5469349319975.1992993779-41.8482178114
575.76427259163-2.198635816190.9016950443145.93321678583-1.001542612086.362870675870.4880181436570.2899197093130.470145244206-0.900479757989-0.4742427516551.06615786023-0.430311727681-0.2696863662770.008223710007870.564362585899-0.00757348972936-0.1482495136630.5405549600070.04062665172680.9353072521655.1800424653872.4943211026-48.1644039262
584.699220422831.150021235542.200840105396.177856421563.488841623762.971840385520.314929264396-0.42688762776-0.2710821504650.321720622671-0.350899275565-0.1124803924741.74684782547-0.3690975568250.3633235290690.674293134149-0.01464094548140.002728517477410.494580554560.09178859568620.9833330131379.4334265611569.5187598954-38.8718804409
598.90772858061.402693525920.2131716794894.54844602875-0.2865366665796.102258483320.138344158525-0.660991355091-1.000231800940.08334765036490.00870220382474-1.901427044240.5381953844680.203776889552-0.1995064788640.591578559110.0272995280606-0.03745909390930.6952123324420.09492423137040.88329352164117.135228335560.0411055864-48.1540773926
602.86237232614-2.4129159909-1.005071480672.550820072661.704428992541.80516853871-0.6771014879031.278165772460.3117410411670.8757133934732.04905400006-0.6909374353491.822684647651.64008297935-1.361987579570.8382446614660.291316567064-0.1401662317051.30699430419-0.1690290694321.3937021157930.177731729652.7358323063-46.4569868595
617.339576028760.843698924443-1.270828456990.531649725372-0.4288730348110.465718551133-0.1923919921770.9931135322761.818101459921.49974639532-0.0346301346709-2.7215832178-0.9569938188742.04280465896-0.8735650730740.07657804087220.111607324927-0.74049116521.641896789070.5074064777292.1950615294129.443587853954.8203824219-40.5946888647
625.404317706170.4539349773611.879990786024.19920969022-2.09325445215.83334169290.3189759252880.385476349109-0.4364916598340.854910437579-0.565262350885-0.180525203733-0.2033306534091.295827932530.4027569955610.576619628668-0.0640863417683-0.03211319840560.4802501036120.04279643223780.74155068134310.955744423471.8793122009-36.5651951837
636.42861524977-0.668907695847-0.06606723386811.959359731260.5054753293874.100357486220.2847430116711.92266949206-0.669627413784-0.305139035668-1.068202847920.05910443972860.650139051262-0.705775674411-1.716992312820.9684399198850.1710351047-0.8642917635930.9677943413080.104616466732.26382942221-11.743758940865.3149427355-57.1577091638
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 'A' and (resid 1 through 108 )AA1 - 1081 - 108
22chain 'A' and (resid 109 through 222 )AA109 - 222109 - 216
33chain 'B' and (resid 1 through 75 )BB1 - 751 - 75
44chain 'B' and (resid 76 through 90 )BB76 - 9076 - 90
55chain 'B' and (resid 91 through 128 )BB91 - 12891 - 128
66chain 'B' and (resid 129 through 150 )BB129 - 150129 - 150
77chain 'B' and (resid 151 through 213 )BB151 - 213151 - 213
88chain 'H' and (resid 2 through 129 )HC2 - 1291 - 128
99chain 'H' and (resid 130 through 224 )HC130 - 224129 - 218
1010chain 'L' and (resid 1 through 18 )LD1 - 181 - 18
1111chain 'L' and (resid 19 through 38 )LD19 - 3819 - 38
1212chain 'L' and (resid 39 through 75 )LD39 - 7539 - 75
1313chain 'L' and (resid 76 through 103 )LD76 - 10376 - 103
1414chain 'L' and (resid 104 through 175 )LD104 - 175104 - 175
1515chain 'L' and (resid 176 through 215 )LD176 - 215176 - 215
1616chain 'E' and (resid 334 through 375 )EE334 - 3751 - 42
1717chain 'E' and (resid 376 through 393 )EE376 - 39343 - 60
1818chain 'E' and (resid 394 through 421 )EE394 - 42161 - 88
1919chain 'E' and (resid 422 through 442 )EE422 - 44289 - 109
2020chain 'E' and (resid 443 through 459 )EE443 - 459110 - 126
2121chain 'E' and (resid 460 through 479 )EE460 - 479127 - 146
2222chain 'E' and (resid 480 through 494 )EE480 - 494147 - 161
2323chain 'E' and (resid 495 through 516 )EE495 - 516162 - 183
2424chain 'E' and (resid 517 through 526 )EE517 - 526184 - 193
2525chain 'F' and (resid 1 through 40 )FI1 - 401 - 40
2626chain 'F' and (resid 41 through 60 )FI41 - 6041 - 60
2727chain 'F' and (resid 61 through 83 )FI61 - 8361 - 83
2828chain 'F' and (resid 84 through 108 )FI84 - 10884 - 108
2929chain 'F' and (resid 109 through 127 )FI109 - 127109 - 127
3030chain 'F' and (resid 128 through 183 )FI128 - 183128 - 177
3131chain 'F' and (resid 184 through 197 )FI184 - 197178 - 191
3232chain 'F' and (resid 198 through 222 )FI198 - 222192 - 216
3333chain 'G' and (resid 1 through 18 )GJ1 - 181 - 18
3434chain 'G' and (resid 19 through 75 )GJ19 - 7519 - 75
3535chain 'G' and (resid 76 through 102 )GJ76 - 10276 - 102
3636chain 'G' and (resid 103 through 128 )GJ103 - 128103 - 128
3737chain 'G' and (resid 129 through 150 )GJ129 - 150129 - 150
3838chain 'G' and (resid 151 through 163 )GJ151 - 163151 - 163
3939chain 'G' and (resid 164 through 174 )GJ164 - 174164 - 174
4040chain 'G' and (resid 175 through 197 )GJ175 - 197175 - 197
4141chain 'G' and (resid 198 through 213 )GJ198 - 213198 - 213
4242chain 'C' and (resid 2 through 34 )CK2 - 341 - 33
4343chain 'C' and (resid 35 through 53 )CK35 - 5334 - 52
4444chain 'C' and (resid 54 through 74 )CK54 - 7453 - 73
4545chain 'C' and (resid 75 through 144 )CK75 - 14474 - 138
4646chain 'C' and (resid 145 through 226 )CK145 - 226139 - 220
4747chain 'D' and (resid 1 through 18 )DL1 - 181 - 18
4848chain 'D' and (resid 19 through 38 )DL19 - 3819 - 38
4949chain 'D' and (resid 39 through 75 )DL39 - 7539 - 75
5050chain 'D' and (resid 76 through 103 )DL76 - 10376 - 103
5151chain 'D' and (resid 104 through 114 )DL104 - 114104 - 114
5252chain 'D' and (resid 115 through 145 )DL115 - 145115 - 145
5353chain 'D' and (resid 146 through 156 )DL146 - 156146 - 156
5454chain 'D' and (resid 157 through 215 )DL157 - 215157 - 215
5555chain 'I' and (resid 334 through 358 )IJ334 - 3581 - 25
5656chain 'I' and (resid 359 through 375 )IJ359 - 37526 - 42
5757chain 'I' and (resid 376 through 421 )IJ376 - 42143 - 88
5858chain 'I' and (resid 422 through 451 )IJ422 - 45189 - 118
5959chain 'I' and (resid 452 through 469 )IJ452 - 469119 - 136
6060chain 'I' and (resid 470 through 479 )IJ470 - 479137 - 146
6161chain 'I' and (resid 480 through 494 )IJ480 - 494147 - 161
6262chain 'I' and (resid 495 through 516 )IJ495 - 516162 - 183
6363chain 'I' and (resid 517 through 526 )IJ517 - 526184 - 193

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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