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- PDB-6zer: Crystal structure of receptor binding domain of SARS-CoV-2 Spike ... -

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基本情報

登録情報
データベース: PDB / ID: 6zer
タイトルCrystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab
要素
  • EY6A heavy chain
  • EY6A light chain
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / EY6a / RBD / Spike glycoprotein / SARS-CoV-2 / human neutralizing antibody / 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 / membrane fusion / Attachment and Entry / 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
PHOSPHATE 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: 3.8 Å
データ登録者Zhou, D. / Zhao, Y. / Fry, E.E. / Ren, J. / Stuart, D.I.
資金援助 英国, 中国, 3件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
Wellcome Trust101122/Z/13/Z 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 中国
引用ジャーナル: Nat Struct Mol Biol / 年: 2020
タイトル: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.
著者: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / ...著者: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / Che Ma / Jiandong Huo / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Robert F Donat / Kerry Godwin / Karen R Buttigieg / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles W Carroll / Javier Gilbert-Jaramillo / Michael L Knight / William James / Raymond J Owens / James H Naismith / Alain R Townsend / Elizabeth E Fry / Yuguang Zhao / Jingshan Ren / David I Stuart / Kuan-Ying A Huang /
要旨: The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID- ...The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (K of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.
履歴
登録2020年6月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年6月24日Provider: repository / タイプ: Initial release
改定 1.12020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.22020年8月12日Group: Database references / Structure summary / カテゴリ: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32020年10月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.42021年2月10日Group: Database references / カテゴリ: citation_author / Item: _citation_author.identifier_ORCID
改定 1.52021年12月22日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name
改定 1.62024年1月24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: EY6A heavy chain
L: EY6A light chain
A: Spike protein S1
B: EY6A heavy chain
C: EY6A light chain
D: Spike protein S1
F: EY6A heavy chain
G: EY6A light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)212,30516
ポリマ－211,2629
非ポリマー1,0447
水00
1
E: Spike protein S1
H: EY6A heavy chain
L: EY6A light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,7375
ポリマ－70,4213
非ポリマー3162
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Spike protein S1
B: EY6A heavy chain
C: EY6A light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,7375
ポリマ－70,4213
非ポリマー3162
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
D: Spike protein S1
F: EY6A heavy chain
G: EY6A light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,8326
ポリマ－70,4213
非ポリマー4113
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)166.404, 166.404, 270.675
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-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 390 or (resid 391...
d_2ens_1(chain "D" and (resid 333 through 390 or (resid 391...
d_3ens_1(chain "E" and (resid 333 through 528 or resid 601))
d_1ens_2(chain "B" and (resid 1 through 136 or resid 142 through 224))
d_2ens_2(chain "F" and (resid 1 through 136 or resid 142 through 224))
d_3ens_2(chain "H" and (resid 1 through 136 or resid 142 through 224))
d_1ens_3chain "C"
d_2ens_3chain "G"
d_3ens_3chain "L"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRLYSE1 - 196
d_12ens_1NAGNAGF
d_21ens_1THRLYSI1 - 196
d_22ens_1NAGNAGJ
d_31ens_1THRLYSA1 - 196
d_32ens_1NAGNAGB
d_11ens_2GLUSERG1 - 136
d_12ens_2GLYCYSG139 - 221
d_21ens_2GLUSERK1 - 136
d_22ens_2GLYCYSK138 - 220
d_31ens_2GLUSERC1 - 136
d_32ens_2GLYCYSC139 - 221
d_11ens_3ASPCYSH1 - 215
d_21ens_3ASPCYSL1 - 215
d_31ens_3ASPCYSD1 - 215

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.503725256508, -0.863829246163, -0.00773947216164), (0.863646985031, -0.503779317886, 0.0178964833741), (-0.0193584917484, 0.00233073888006, 0.999809890156)244.678958271, -45.5952266928, 1.83740466962
2given(0.999443753898, 0.00849620564558, 0.0322489888905), (0.00864238995191, -0.99995298969, -0.00439630589198), (0.0322101209366, 0.00467256880151, -0.99947019726)2.52812864599, 99.060710072, 86.3240533058
3given(-0.506677047039, -0.862135932254, -6.57260416658E-5), (0.862089814416, -0.506650729204, 0.0103048763879), (-0.00891750435839, 0.00516458258726, 0.999946901192)244.31708008, -44.8252884783, 0.748293492863
4given(0.999487846917, -0.0078787257353, 0.0310156338962), (-0.00792913922222, -0.999967434698, 0.00150276235074), (0.0310027840103, -0.0017479199856, -0.999517769807)3.32682827586, 100.154429414, 86.7294961904
5given(-0.504133096728, -0.863620084229, -0.00318918489888), (0.863597794048, -0.504143041122, 0.00621644621058), (-0.00697645317361, 0.000379743235292, 0.99997559215)244.336459464, -44.6014116893, 0.668028428849
6given(0.999762549465, -0.00668067123796, 0.0207415842924), (-0.0066897229277, -0.99997755619, 0.000367047717124), (0.0207386666471, -0.000505716013445, -0.999784802824)4.07199870376, 100.153166487, 87.7013075156

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要素

#1: タンパク質 Spike protein S1


分子量: 22758.518 Da / 分子数: 3 / 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
#2: 抗体 EY6A heavy chain


分子量: 24346.273 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#3: 抗体 EY6A light chain


分子量: 23315.855 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#4: 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: 3 / 由来タイプ: 組換発現 / 式: C8H15NO6
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
#5: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 4 / 由来タイプ: 合成 / 式: PO4
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: 5.12 Å3/Da / 溶媒含有率: 75.98 %
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: 0.02 M NaH2PO4, 0.98 M K2HPO4

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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4月15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: 3.8→144 Å / Num. obs: 43446 / % possible obs: 100 % / 冗長度: 19.8 % / Biso Wilson estimate: 158.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.227 / Net I/σ(I): 7.3
反射 シェル解像度: 3.8→3.87 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2141 / CC1/2: 0.783

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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: 6YLA

6yla


解像度: 3.8→28.22 Å / SU ML: 0.6321 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 31.9594
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2511 2157 5 %
Rwork0.2119 40965 -
obs0.2139 43122 99.67 %
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: 185.24 Å2
精密化ステップサイクル: LAST / 解像度: 3.8→28.22 Å
タンパク質核酸リガンド溶媒全体
原子数14585 0 62 0 14647
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003415000
X-RAY DIFFRACTIONf_angle_d0.609420401
X-RAY DIFFRACTIONf_chiral_restr0.04572255
X-RAY DIFFRACTIONf_plane_restr0.00522616
X-RAY DIFFRACTIONf_dihedral_angle_d27.00475850
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2EX-RAY DIFFRACTIONcartesian NCS0.00524142383094
ens_1d_3EX-RAY DIFFRACTIONcartesian NCS0.042176090118
ens_2d_2GX-RAY DIFFRACTIONcartesian NCS0.00647064874935
ens_2d_3GX-RAY DIFFRACTIONcartesian NCS0.0311407593934
ens_3d_2HX-RAY DIFFRACTIONcartesian NCS0.0161221297095
ens_3d_3HX-RAY DIFFRACTIONcartesian NCS0.0161292050742
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.890.42331370.39482692X-RAY DIFFRACTION99.4
3.89-3.990.38741400.36282697X-RAY DIFFRACTION99.75
3.99-4.090.32771570.31382641X-RAY DIFFRACTION99.71
4.09-4.210.32981550.2832713X-RAY DIFFRACTION99.83
4.21-4.350.29841210.25942737X-RAY DIFFRACTION99.86
4.35-4.50.27161240.22022732X-RAY DIFFRACTION99.83
4.5-4.680.24151430.19562703X-RAY DIFFRACTION99.75
4.68-4.890.25321720.19792690X-RAY DIFFRACTION99.83
4.89-5.150.20871560.1962686X-RAY DIFFRACTION99.68
5.15-5.470.23231230.19632724X-RAY DIFFRACTION99.72
5.47-5.890.32341340.20622784X-RAY DIFFRACTION99.79
5.89-6.480.26441390.2182747X-RAY DIFFRACTION99.83
6.48-7.40.22411400.19772768X-RAY DIFFRACTION99.86
7.4-9.270.22041670.17442780X-RAY DIFFRACTION99.8
9.27-28.220.20351490.17752871X-RAY DIFFRACTION98.76
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.10903078304-0.2331608297713.163190777968.079609539846.063700532386.30471260931-0.00750961780108-1.61428806274-0.7565932278241.160929090270.110729060023-0.4692116383080.719490980669-0.727102069363-0.9100940001911.54070158048-0.145227758652-0.1931275371271.149213877630.2279076963961.62532532573104.156245129.7849210133.5628092414
26.166925310134.984960372996.472567682199.011195909842.406902027066.56067739465-0.0351333798716-1.18728465650.7235650258940.5945678624420.1122423204011.807535993750.051902056014-0.680594220645-0.3171822625831.301636674210.01090334630630.4476581720591.453015921650.04322452658081.8750024822297.405827202537.690564933225.8175229168
34.54590393142-1.946856387364.440776100345.40540793072-1.290910111443.19150561925-0.6542059755440.1308510862431.089142529130.8068153574470.8004435496811.06143027517-0.214147513410.0893765178304-0.1309657189641.60228709014-0.2494130928610.2605298695481.25385830642-0.04440799080061.08804309251112.96895327139.15044171926.0249919821
42.196079965690.6981457928170.7193932991765.149643771820.3055570800341.904946822820.505222529083-2.91390351105-1.115522386232.5490935793-0.04154540678362.85063405685-1.64291541209-1.22774712596-0.2938944204632.904433568890.09892404989430.526778257762.13222846169-0.1194416003741.2145051574116.13136476135.822596252145.5031270834
58.8828320693-2.752975360070.9366863100885.11479674209-3.290020061921.3334593994-0.4274893603811.058065643750.8448130192060.7906288077260.285035699975-1.3679895507-1.524409294660.7548759165210.02292210848351.68001468151-0.00654810363327-0.1752272991561.25815882151-0.08962431662141.22866004844130.29410203629.682370967727.2743073957
64.79358598601-3.293711024123.663825066586.7036761657-0.8762699430722.96673791619-0.157177600458-0.001260726648880.402759862081.531529183870.496923429032-0.3507459745890.8662718806250.160490017717-0.3591642262472.31058366432-0.04922450962130.4808559897491.378032434170.1298383941291.28710366052113.20463538340.126960622936.4968809799
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111.726163278082.429781300232.681763839361.317797138690.3569743219979.31783115786-0.3837444597440.194573795270.771769906480.4927072429130.325754548469-0.0160185540254-0.183104510551-0.4778763393930.05895764090831.212063385890.2930238568550.4142118221791.287260315390.2951403430731.67015643401103.70418446196.043148556417.8092082533
121.81206606827-0.496006483278-1.073094579367.87323610718-3.220420584852.267787692510.3981057309030.0045796473212-0.0256583778691-0.18179037544-0.3964398834750.845637249442-0.3139211262290.447053265065-0.1017433092761.751014338460.0104876149790.1129527178991.243650773090.1370465232591.4865311589108.31590118459.4506573686.01594385418
136.549722239810.1761379425523.616751486987.132979864772.897368070924.610788529280.05568733455440.0624704191291-0.382467469659-1.44271045132-0.07469902231042.58862037810.434367288978-0.575390157198-0.678871208191.720729550490.00758794024353-0.1527799746141.076094375650.2686400673451.9655560218499.748050096458.75297034862.80346624929
145.685943576961.184772663023.1415643349.310890386330.09743356989311.83921925279-0.2672083396610.509131123338-0.0750982563281-1.651030706240.6206649138061.686697109170.7133111461930.673343690772-0.272934086261.413834669840.079447601149-0.1433778533830.884458077207-0.1525286621.6923554282105.42253549966.47646513385.45677263085
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174.215318767011.060901442861.871228231977.658384316732.022670070335.06322065895-0.126179086574-0.424183070018-0.09305303932390.7195062270090.9876744506390.155547718868-0.683156046714-0.0315468841855-0.5582642393641.30062402690.2612172991580.1851755364271.134572550340.2028973537961.26285881011119.59687354291.005334274714.0486641464
188.950510963171.06453427562-2.535323940018.994061113153.988149364773.46186824984-0.02730422950021.50046431321-0.488279906696-2.275633487290.228214127948-1.1604485187-1.35463689721-0.22109580739-0.07972719413972.331214491210.1656337188460.4260123891211.087399653020.01834042033561.4574619567299.273430690169.890207470956.3145278219
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256.787352846971.916769411340.09342543323725.57544305322-4.380974381363.28759767873-0.380132276921-0.6733186709280.068697100425-0.410787386813-0.9284983606210.1812326349491.504119762330.689266843360.8149807545872.446572059350.161113984140.64136601211.71294778599-0.03096039721332.45417472334131.37750264971.48078628961.4384832242
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284.444122636844.920186900021.381051554665.121164116741.849917793253.132800076321.18876656095-2.078388080080.0624951079637-2.60874907416-1.42348915937-1.91611032273-0.195514502065-3.560513730772.113432210891.717595684270.299256064358-0.4548420903761.70111278286-0.1512397824312.3829026140987.869986602269.823629783274.0388718848
293.215628283863.48166676768-1.761334616974.924990928170.146664127053.40957645103-0.559519308811-0.1202524880641.300655074270.2725457544860.6247118691060.587063009717-0.146506976498-0.0705718707502-0.3836638453361.407613056950.110638442601-0.3147870687521.530685005740.1219144481392.2330607132686.974151895835.805674218365.9392174874
303.976458193651.62313839911-1.117541855477.63128685728-0.3835185849764.713118192290.2031126573520.1721618202813.71256286698-2.036221091551.324290237041.7195967576-0.89249595375-0.675397398009-0.7287499934141.65806771309-0.0068073670504-0.2513744371251.627790676440.2729328723742.4904272722190.958597128146.485469703760.200041757
310.629412052541.836677354060.2933086097678.96115374209-0.1722449028825.72047699107-0.421789436903-0.114595803282.13116539363-1.055399673151.291353870870.9491305554930.4311094794-0.175541677925-0.4144524526491.39666810473-0.0750993718401-0.2865259060791.8593303810.2654691147192.4335374706986.912772630737.235382842258.917086061
323.141860578153.25200000151-1.433174993994.5645595861-1.211078903332.84752938798-0.40640360046-0.1370826442491.464644473520.1963971749190.2577234218681.92404574399-0.761942800266-0.613797042932-0.5138531048531.341691421120.2067148103670.1338903873621.32349323913-0.03157611290782.2028573254689.076981067243.746879282273.1460775569
332.47161354793.97298454666-1.481676845795.99162674905-1.140689923180.903266248234-0.1844183672530.1569515334310.868094868295-0.1550366892120.4609827182051.045778276630.24261125563-0.520017225847-0.1141693197561.40941954053-0.0485194917651-0.2579527819031.467301875820.3106642627451.5873073520591.419758908224.931361069464.8742677498
346.53958827999-0.8386923953342.214921155787.471919818560.7154350612651.893204406430.5825200514890.550111722687-1.06159456527-2.518401133921.303759313991.411200980190.596989065083-0.941134826201-1.722347946761.424312504070.119583730335-0.3118375373821.58863463297-0.02263605951291.15830011671107.524820004-2.1753256483775.1932211829
351.25569219467-2.65761753591-0.2376278206633.687803644641.731491347685.8166528419-0.1456897673670.0667172150046-0.950723709055-0.8453985250270.224030720778-0.71869584526-0.0434471795707-0.422409182736-0.2690955789721.39927373734-0.172203304336-0.1931263917511.193646861290.0008293701920841.7601637711798.43454552387.9733260818871.3700704452
362.85170799433-1.59868502428-3.865512198378.22438329574-0.5970022898194.56015402956-1.14916556081-0.293269507839-1.27888064568-0.4409597982590.6358809732280.962102577541.049667914350.236185434740.192016509221.32637896111-0.004662488438440.07844429145270.9267175863630.1030427353321.7799725361498.5873156152-0.043369221697775.9600774588
376.46137309878-6.244086609041.544057205665.05083178562-0.1950548444459.69509652155-1.719232753290.637942918759-0.4358704207441.364054060730.8794769356780.0862958637027-0.0483442192269-1.081343360680.2093942017221.79622319855-0.411611135448-0.4758416980821.238649200420.1093906337992.3114833947497.1829424994-2.0559391404967.6055022598
384.86987164402-1.66617312619-0.3204485597313.43152538019-0.8759213313652.933307439330.199575326-0.212693588314-0.2434530559010.6413285689270.05955475710351.774191222490.180966672730.31143151988-0.2693114886561.63809809090.1591973148550.1214836734891.03595901609-0.01445492552341.7444773447299.132664495137.843132724484.9174610904
392.87522678159-2.30506371362-5.171100129537.472395290632.370302257087.22999648411-0.1184511894810.2435736306160.105022847029-0.05636088646210.05479925751190.420938671921-0.0530668248797-0.537554087404-0.1596321439571.23525865956-0.140947811901-0.207273054771.09575286432-0.02260868553051.62038394201113.7092036058.5315760507274.7830817844
405.435195347190.290392965867-1.593589896347.19038700108-3.363954901496.66685506443-0.4439312545110.408046751845-0.0722930904698-0.01127344468760.0916821733041-1.079234220280.423747197157-1.060018791770.2786198211841.25088983895-0.1422107248-0.2335074048031.40913857354-0.1139571435342.08805704059134.1800120973.8612634917659.078126053
416.95955698565-1.065264361314.895304916659.82656985502-6.857869555358.832925245160.06401727814021.09230043242-0.6603660824360.559070167058-0.567120931-0.661503204612-0.2279913332430.1742027867390.3057815895991.27733435602-0.0225963174336-0.05108594390821.11791679659-0.2836579023681.14744611999142.31323800412.624633925363.5292385523
425.553797453441.41681842864-0.3791210882665.67940255821-0.9481502328572.03250058009-0.1514612061010.7189029547090.0626502286457-0.333502685070.220322894342-0.464621507339-0.250376337015-1.08566638889-0.05294028492961.56410489040.0493784897206-0.2192857292791.48959509945-0.177068014521.4297716411132.02649001319.373993750459.824262052
439.246746553080.5057809260082.558746956169.189891469542.599370480012.42889910825-0.4429773413490.961575465065-0.04162550145580.4527051934940.3643871431151.826839428860.05621812678570.807257186364-0.5034228599541.30926107115-0.0716759382862-0.1063737271551.892670336250.2801868379562.05171099441116.27891078332.95732029360.8886419301
445.1218700043-1.59327992879-2.099669374477.03355357006-10.37071011678.957789431720.4064990117180.340229398995-0.78038203465-0.5644002129340.5978517694991.052841002360.61040291647-0.360688359846-1.076416707881.7239275212-0.360144946437-0.2084489405551.17413014081-0.2844726236831.71436039366138.53687868912.023838468259.9533021731
457.137279836-0.5097429082421.627302474711.51225093718-0.3525937865435.942207016560.599463555921.36471247515-2.232340895250.2860147254910.004851318840720.04167324754210.6737442998350.647311123926-0.5206790894181.462142360150.193045032649-0.3902083752251.20665749759-0.5862645101552.32491258054166.09476929711.833634257964.8326609275
468.183229794342.70740597922-1.963773134962.442396354941.071869013431.8005809691-0.4905511008591.01800733166-2.35648124876-0.6154409226370.270096333195-1.653455100540.844761752056-0.335158591197-0.0485960112671.079075556230.0363979493792-0.2436868988521.5690459588-0.4471197718761.94648709634176.49705627622.024859894864.9321700794
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495.287594166992.57952244011-0.9180900050825.86989072474-4.677572513267.742299823190.1925685923951.08271025627-0.437884503020.09342211376780.0147612618289-0.138811872337-0.0406842147098-0.123929267067-0.3397713810610.8634773447230.1290318485170.03380448620231.41084884351-0.1767091507781.14335666993179.40571309449.762084067974.6591467371
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 353 )EA333 - 3531 - 21
22chain 'E' and (resid 354 through 393 )EA354 - 39322 - 61
33chain 'E' and (resid 394 through 437 )EA394 - 43762 - 105
44chain 'E' and (resid 438 through 451 )EA438 - 451106 - 119
55chain 'E' and (resid 452 through 494 )EA452 - 494120 - 162
66chain 'E' and (resid 495 through 516 )EA495 - 516163 - 184
77chain 'E' and (resid 517 through 529 )EA517 - 529185 - 197
88chain 'H' and (resid 1 through 91 )HC1 - 911 - 91
99chain 'H' and (resid 92 through 108 )HC92 - 10892 - 108
1010chain 'H' and (resid 109 through 142 )HC109 - 142109 - 139
1111chain 'H' and (resid 143 through 224 )HC143 - 224140 - 221
1212chain 'L' and (resid 1 through 38 )LD1 - 381 - 38
1313chain 'L' and (resid 39 through 75 )LD39 - 7539 - 75
1414chain 'L' and (resid 76 through 114 )LD76 - 11476 - 114
1515chain 'L' and (resid 115 through 151 )LD115 - 151115 - 151
1616chain 'L' and (resid 152 through 161 )LD152 - 161152 - 161
1717chain 'L' and (resid 162 through 215 )LD162 - 215162 - 215
1818chain 'A' and (resid 333 through 353 )AE333 - 3531 - 21
1919chain 'A' and (resid 354 through 380 )AE354 - 38022 - 48
2020chain 'A' and (resid 381 through 393 )AE381 - 39349 - 61
2121chain 'A' and (resid 394 through 421 )AE394 - 42162 - 89
2222chain 'A' and (resid 422 through 437 )AE422 - 43790 - 105
2323chain 'A' and (resid 438 through 451 )AE438 - 451106 - 119
2424chain 'A' and (resid 452 through 469 )AE452 - 469120 - 137
2525chain 'A' and (resid 470 through 494 )AE470 - 494138 - 162
2626chain 'A' and (resid 495 through 506 )AE495 - 506163 - 174
2727chain 'A' and (resid 507 through 516 )AE507 - 516175 - 184
2828chain 'A' and (resid 517 through 528 )AE517 - 528185 - 196
2929chain 'B' and (resid 1 through 51 )BG1 - 511 - 51
3030chain 'B' and (resid 52 through 67 )BG52 - 6752 - 67
3131chain 'B' and (resid 68 through 91 )BG68 - 9168 - 91
3232chain 'B' and (resid 92 through 108 )BG92 - 10892 - 108
3333chain 'B' and (resid 109 through 127 )BG109 - 127109 - 127
3434chain 'B' and (resid 128 through 142 )BG128 - 142128 - 139
3535chain 'B' and (resid 143 through 183 )BG143 - 183140 - 180
3636chain 'B' and (resid 184 through 208 )BG184 - 208181 - 205
3737chain 'B' and (resid 209 through 224 )BG209 - 224206 - 221
3838chain 'C' and (resid 1 through 114 )CH1 - 1141 - 114
3939chain 'C' and (resid 115 through 215 )CH115 - 215115 - 215
4040chain 'D' and (resid 333 through 364 )DI333 - 3641 - 32
4141chain 'D' and (resid 365 through 421 )DI365 - 42133 - 89
4242chain 'D' and (resid 422 through 469 )DI422 - 46990 - 137
4343chain 'D' and (resid 470 through 494 )DI470 - 494138 - 162
4444chain 'D' and (resid 495 through 528 )DI495 - 528163 - 196
4545chain 'F' and (resid 1 through 108 )FK1 - 1081 - 108
4646chain 'F' and (resid 109 through 127 )FK109 - 127109 - 127
4747chain 'F' and (resid 128 through 224 )FK128 - 224128 - 220
4848chain 'G' and (resid 1 through 114 )GL1 - 1141 - 114
4949chain 'G' and (resid 115 through 215 )GL115 - 215115 - 215

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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://pdbjlc1.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