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- PDB-7nx8: Crystal structure of the K417T mutant receptor binding domain of ... -

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基本情報

登録情報
データベース: PDB / ID: 7nx8
タイトルCrystal structure of the K417T mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs
要素
  • (COVOX-222 Fab ...) x 2
  • EY6A Fab heavy chain
  • EY6A Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 B.1.1.7 variant / B.1.351 variant / P.1 variant / antibody / receptor-binding-domain / spike / neutralisation / 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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
CITRIC ACID / DI(HYDROXYETHYL)ETHER / 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: 1.95 Å
データ登録者Zhou, D. / 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: Antibody evasion by the P.1 strain of SARS-CoV-2.
著者: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Lopez-Camacho, C. / Slon-Campos, ...著者: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Costa Clemens, S.A. / Naveca, F.G. / Nascimento, V. / Nascimento, F. / Fernandes da Costa, C. / Resende, P.C. / Pauvolid-Correa, A. / Siqueira, M.M. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S.C. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Hulswit, R.J.G. / Bowden, T.A. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
#1: ジャーナル: Biorxiv / 年: 2021
タイトル: Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2
著者: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Paesen, G.C. / Lopez-Camacho, C. / ...著者: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Paesen, G.C. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Clemens, S.A.C. / Naveca, F.G. / Nascimento, V. / Nascimento, F. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Hulswit, R.J.G. / Bowden, T.A. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
履歴
登録2021年3月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年4月7日Provider: repository / タイプ: Initial release
改定 1.12021年4月28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
改定 1.22021年6月9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 / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
H: EY6A Fab heavy chain
L: EY6A Fab light chain
E: Spike protein S1
A: COVOX-222 Fab heavy chain
B: COVOX-222 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)120,08933
ポリマ－117,5745
非ポリマー2,51528
水5,747319
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16650 Å2
ΔGint-253 kcal/mol
Surface area44070 Å2
手法PISA
単位格子
Length a, b, c (Å)54.843, 122.727, 213.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

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抗体 , 4種, 4分子 HLAB

#1: 抗体 EY6A Fab heavy chain


分子量: 24346.273 Da / 分子数: 1 / 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 EY6A Fab light chain


分子量: 23315.855 Da / 分子数: 1 / 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-222 Fab heavy chain


分子量: 23461.182 Da / 分子数: 1 / 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-222 Fab light chain


分子量: 23327.857 Da / 分子数: 1 / 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, 2分子 E

#3: タンパク質 Spike protein S1


分子量: 23122.814 Da / 分子数: 1 / 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: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H15NO6
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 , 6種, 346分子

#7: 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: 3 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C4H10O3
#9: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 12 / 由来タイプ: 合成 / 式: SO4
#10: 化合物 ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H8O7
#11: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Cl
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 319 / 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
Has protein modificationY

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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: 3.06 Å3/Da / 溶媒含有率: 59.81 %
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
詳細: 0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000.

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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: 0.9762 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年2月23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: 0.9762 Å / 相対比: 1
反射解像度: 1.95→81 Å / Num. obs: 106251 / % possible obs: 100 % / 冗長度: 13.4 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.034 / Net I/σ(I): 12
反射 シェル解像度: 1.95→1.98 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5188 / CC1/2: 0.354

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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
GDA1.19_4092データ収集
xia2データ削減
xia2データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7NX6

7nx6


解像度: 1.95→80.62 Å / SU ML: 0.2956 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.9217
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2458 5255 4.96 %
Rwork0.2232 100792 -
obs0.2243 106047 99.88 %
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: 75.18 Å2
精密化ステップサイクル: LAST / 解像度: 1.95→80.62 Å
タンパク質核酸リガンド溶媒全体
原子数8003 0 140 319 8462
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00178323
X-RAY DIFFRACTIONf_angle_d0.477611319
X-RAY DIFFRACTIONf_chiral_restr0.04131248
X-RAY DIFFRACTIONf_plane_restr0.00461443
X-RAY DIFFRACTIONf_dihedral_angle_d11.29012950
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.39971730.38053211X-RAY DIFFRACTION97.19
1.97-20.37321790.35593252X-RAY DIFFRACTION99.97
2-2.020.31331590.33783343X-RAY DIFFRACTION99.83
2.02-2.050.31931820.32543358X-RAY DIFFRACTION99.89
2.05-2.070.31951710.31183278X-RAY DIFFRACTION100
2.07-2.10.33181840.30543331X-RAY DIFFRACTION99.97
2.1-2.130.35031710.29993315X-RAY DIFFRACTION100
2.13-2.160.32711630.29893344X-RAY DIFFRACTION99.94
2.16-2.20.32791880.31043366X-RAY DIFFRACTION100
2.2-2.230.33611650.29813289X-RAY DIFFRACTION100
2.23-2.270.33951650.27983347X-RAY DIFFRACTION99.97
2.27-2.310.28591640.26633332X-RAY DIFFRACTION100
2.31-2.360.28031770.25173346X-RAY DIFFRACTION100
2.36-2.40.26861600.24863356X-RAY DIFFRACTION100
2.4-2.460.28431940.23733312X-RAY DIFFRACTION100
2.46-2.510.27081750.23283345X-RAY DIFFRACTION100
2.51-2.580.25091770.23033336X-RAY DIFFRACTION99.94
2.58-2.650.25991820.24633330X-RAY DIFFRACTION100
2.65-2.720.28041660.25413378X-RAY DIFFRACTION99.97
2.72-2.810.29611520.25053363X-RAY DIFFRACTION100
2.81-2.910.26231840.23893359X-RAY DIFFRACTION100
2.91-3.030.2641770.22213373X-RAY DIFFRACTION100
3.03-3.170.23851640.21933383X-RAY DIFFRACTION100
3.17-3.330.23261770.21313376X-RAY DIFFRACTION100
3.33-3.540.22681770.20573402X-RAY DIFFRACTION100
3.54-3.820.24111800.19913383X-RAY DIFFRACTION100
3.82-4.20.16121670.17063457X-RAY DIFFRACTION100
4.2-4.810.18371990.15213396X-RAY DIFFRACTION100
4.81-6.060.221910.18423488X-RAY DIFFRACTION100
6.06-80.620.27211920.26653643X-RAY DIFFRACTION99.71
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)
15.81701238894-2.741254177030.8153473093771.520248347630.3721003032854.473105003560.562216882186-0.8684212754741.000590860341.41311786884-0.110727186452-1.96251865585-0.2831104099041.01161856811-0.6058949981151.74406646632-0.240107902319-0.4847178167361.03288321187-0.3296242663811.5187723184632.7971019408-13.83935813-10.143629808
27.26434958504-0.197969267361-1.984220696493.889353216482.296250965664.339220957710.3828855031-0.4866990643771.421245420241.364077722130.200803138946-2.02477197196-0.6301053088140.742556980221-0.4944460219371.21016779112-0.13293122653-0.2451260951460.594014668229-0.0796445472991.16839007328.3933411051-18.4154286069-15.4956645699
33.51722742377-0.332787762582-1.151274996414.524914305940.520962320525.610848281140.5924772849650.3001436346143.15301592118-1.055212238361.24921908334-0.68946220004-0.930891189379-0.418203221374-1.585388818741.42939742582-0.374265091720.008740633565961.008973387910.4608857672741.5399954457115.692158129914.6063655559-16.1332558874
42.81573786279-0.2324262070581.515210406187.4003322306-1.762823935113.598798203060.396148809496-0.4935390111041.866116151040.329844701867-0.5245941273650.0620366836672-1.262422347111.54531405765-0.2123991936791.88195703654-0.03710641125080.007376440120450.9958159864930.212212577761.5770164844516.09403994911.0994724174-12.2543549899
51.539025483320.0720054200464-0.3648220207457.798049408023.159135729254.84101837031-0.0166008144076-0.5454436428050.9714231545521.390660926310.335886511280.120125467692-0.0710547898279-0.392083740254-0.5679683344042.206094930980.1064260412460.280340119770.851085322232-0.0601314007551.5415884657710.333517640512.4826224234-7.69999482751
60.7157536811510.1125719366680.3594141743983.55262671637-3.727944316966.67768061008-0.098908025953-0.06193602311920.3321986868831.47125514567-1.690297360780.725668268448-0.0707156756556-0.02089375626781.571440552271.30938680677-0.04402498486250.2907513623171.02171074688-0.2103928274312.209150186819.879805909716.9235114943-7.87424365024
73.16092627571-1.60421897448-2.80462288661.667056114962.958962545325.215135838270.4055154283790.2804175533540.2827368449780.37869717846-0.3439125264390.701154321318-1.18340455869-0.786715653731-0.2381042389831.215103738020.09493993288030.3425707392240.4705659379740.01143813502870.6358995613353.23468621801-19.2883021534-11.1147968019
82.25087179981-1.32438346299-2.112040623713.835838933413.24317317273.629806331790.01431724625260.1108406504730.1023413189071.944437468140.4059071377810.57388149833-0.0955937511717-1.150448235890.4066925884781.353639633740.1367403681090.2924978382960.373508928584-0.07889339785310.4361925929439.62429660914-26.4106298733-12.4562835046
92.062766647750.129331906657-0.8875750293151.356807027180.6774918516540.7549088121970.00804977810985-0.3475682767190.5460278523311.191885231510.281538046920.382941360566-0.355580193801-0.066150259375-0.2405912590511.562964613430.1132036034590.2876175849180.5706659565070.002747975834430.6999805719848.40090282175-17.7386357397-6.78363389941
101.923731584441.03286825636-1.569353752963.731354073221.664360055573.02124426199-0.3259633576670.6492964302681.576980980430.387620918102-0.203554974992-0.0223980167929-0.2715836368640.1993930597340.254974605651.683989032850.08187837161410.1234732658210.8638869387360.6941767453542.153358659896.9421468769816.9890546504-18.1586316258
118.86271718795-0.7373878307021.650897214821.402104635211.675877062312.70098792535-0.8569122156220.95977325940.06377225215780.5137349677270.2262380249450.3528432418120.421791655801-0.4743910679130.8710576827021.41589341732-0.0930047767376-0.008177431444471.159848040990.1241523310851.01661277183-3.440438615453.85825759318-18.6443538909
125.697949670211.23962837496-0.4647379805540.5552572436930.6997010972012.30115623876-1.462479626671.054242134341.060745910851.234500269410.2969605215510.1774974150710.38997450022-0.2857366079161.203681189221.618950653190.0713287331525-0.1847356720731.046104499850.3662455111661.217286993380.9117055230388.59591096436-26.1811245336
139.324614819090.263349864628-0.3564267392654.7312875934-4.76750223254.52242594481-0.226085439642-0.1527784611021.623731192790.3470978492720.308644879984-0.236772956031-0.475185392062-0.453647243735-0.07170506280421.48058629890.1803634273540.2015358971930.6654116246830.100625203761.228213918333.8726329774.58416914505-11.2812797496
144.50615149378-0.5776298558364.916113094050.517103195943-0.3441565354445.5416675072-1.003450358192.229684574931.40805944790.04385861311861.440353499770.976511027846-1.03137715739-0.729130368966-0.4548797329561.89794880543-0.01101732108140.2043050795762.041543328020.9931969178052.08978103697-0.78835896383816.9175189698-26.2461747404
150.2308651357190.505210685474-0.1820792361221.72810312566-2.765663061977.69871213333-0.3371403923450.781998555911.32595875085-1.268494353260.4158732791970.6018888926170.593803877896-0.80738864171-0.6259751866621.596010894120.3155860568320.18991546971.284633324020.6094235502522.38858688675-8.1957269614213.3328414521-17.6065316899
162.24137732677-0.3231472342941.759917274510.705746833314-1.32864937236.403134333170.161534379875-0.05471850822030.0388538378911.03081324648-0.31086699127-1.21543043190.65701769730.9285847572210.1883807028260.7682599025120.0952401471949-0.372521606180.5640052936850.007791272077380.71362556022333.2753472346-47.5531833344-28.5655119752
171.19943666446-1.513659486721.046799152762.07980560566-1.970397469892.987457401770.0272622095831-0.5276795532440.5624306922951.777340520320.02546572763-1.80050747735-0.8312329904431.894481945360.4598601435611.09254534187-0.25471864036-0.4618857029911.018911942780.04109647366161.0357693344936.096524017-34.784534892-24.2519021081
181.68738317848-0.4599228365410.6763591428953.512256186230.07563257016072.443544275370.0866844756551-0.2909223774350.06251214455621.00820785984-0.121222884208-0.303354319402-0.1693873148840.2181467483190.0520554265610.481837892556-0.0612767146144-0.1060391096150.3359194772650.01321858091120.32420131391323.7600978743-38.7157906565-28.7263709824
191.790674949250.3023816531790.6775855376872.8447864517-0.3395561546252.118293116330.07910089084460.29487927743-0.0944448176739-0.1715559216530.0105159583202-0.05037082739210.2662401879070.192590085105-0.07619487314350.2867526365940.0253706470422-0.03175391387070.316906520128-0.03028819168550.31850723908618.0017831267-45.263039547-47.0442151053
201.64510957754-0.9143927198740.05541913805374.31723081805-1.597919513941.78831488248-0.162671453313-0.4798016305190.1737922393681.96152385479-0.429048042689-1.01666774868-0.415615274775-0.01816270814570.2600074998091.01558589819-0.148602964488-0.2721794733480.553313213727-0.05245174794690.36454636324427.5538051927-45.2775882498-21.3438003353
218.4829741905-6.60883362491-3.890839517766.782070070511.330473572374.499882955160.06083516117050.2357142561-1.00484562821-0.446108639723-0.3566100448491.43663797545-0.198036770488-0.5927085183580.3916547908350.119929987911-0.017662925613-0.02583496314860.4257808978370.08937487625530.398438671453-9.81377707494-29.416295496-50.683625142
222.43353194043-2.196481107871.240363133472.52816517044-0.8989870980580.606384857519-0.002737080771010.00304935204258-0.1801635056870.0741699545910.04993297407060.169664798931-0.0296526364436-0.149738931679-0.06472959471880.248330525383-0.004809293233110.02450645398750.3443969001090.01161909799240.323742754537-1.68282999438-30.3721453911-47.9375009251
232.96956102093-0.0820971503983-0.4829653733043.3517921381-0.07292470529542.7924432105-0.1062637216730.138680607905-0.318318135637-0.32025641179-0.0347958308890.2752661551040.2065193005060.01937900004850.1195862850020.2699428833480.0154313936424-0.03671098149420.26059280221-0.009528261566240.364545881882-19.5697364021-20.4315428965-71.4092094991
245.729296275510.9853568344883.185402737724.76320140813.117301641013.09061290796-0.0179009932240.4290035455920.660658097035-0.0253038920995-0.3146364834870.0568404060128-0.1519686522340.4002586061970.3444422121730.1980872754490.04126733744480.03645175807370.3204962169480.1083195097420.36347209555715.645877853-19.1444653099-66.0525803385
257.40009631286-2.531060756241.624640821614.23534686392-0.6836675533764.73923456357-0.009360372508360.4971195000440.8011313190820.228311999291-0.230026451262-0.391372994043-0.1232636123060.836806084770.2935636074380.246271564203-0.02557294290240.01537322571540.406687949910.07390211256970.44217603867922.3352190255-22.4669534131-58.3752011081
266.0102757477-2.285816575310.4703989752612.67986091822-0.8021436469933.560059976450.2549190034780.670022005486-0.196833046629-0.335228355497-0.306825570646-0.06366141031480.2890137352130.1029640520030.03727810842830.2755240009230.04620017908790.01267625103520.3308735803250.01917367538810.24288052742213.989955066-30.5579590231-64.1183624604
271.3114863217-0.7550479808871.586246049682.45735016394-2.503263752115.754022232940.2018657314560.103141496333-0.0260006899486-0.0745837219869-0.1833072011140.0123142534671-0.0424779355735-0.0504759105733-0.03864297323250.244203632770.05360747561080.04128575744440.377537847376-0.004946578440650.34331580577711.0224106257-25.9240214381-61.9006451417
282.64801843646-1.827627136310.7452242378052.16677507718-0.7408869905791.907390245960.09821462426780.463596183719-0.104293486009-0.214016791895-0.1575229788010.128833935643-0.0008703606958990.0493050568110.08368556708190.3130908651220.00603451720589-0.01625058236360.230561599805-0.004957887706210.27853765124-12.7224229993-11.9027991616-75.2576604003
294.81723095596-6.12090116772-3.111581792568.007762541733.482230096572.219306084650.3066696703260.4021164330080.481976769139-0.557818165935-0.326924214399-0.407264997939-0.2902850438690.280880038771-0.0223379583470.409472243684-0.0181836663315-0.01935965424290.4376416151490.1188132260650.399008484751-7.43015971698-4.60000147752-78.1125868545
303.97681104074-4.255162188640.2307567808628.46302478945-2.419445429724.48503068381-0.07856688363570.4069768037330.446687336297-0.113514024402-0.285240775623-0.520647311902-0.7106592266210.07032400175220.3397570379290.397216775843-0.0537394049134-0.09396983269690.258871807398-0.0002199269769950.253101710808-15.48895141210.147954309345-72.7282012199
316.1674308299-2.93051435634-0.8935040544644.119673194350.4709735856962.262882125290.1152613480830.1128620948730.244895930489-0.200980607895-0.1210473753470.0855887981574-0.2165525168070.0691668473046-0.02079238809960.3318510970330.000627829073426-0.02605693770410.2862707426620.0258755624250.257660670761-15.4392427214-6.86235477156-75.8787130344
323.0765939657-2.64250714687-2.606776241255.09540127263-0.4396697778865.003769594330.576537301741.35358440409-0.325072657697-0.678879702494-0.481384396609-0.00764467532441-0.197749243195-0.3895075737310.06073840897060.5548606762520.0223432871995-0.1103677878990.3633962142490.04199188249360.340745615622-16.915755788-3.14568392367-85.31619328
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 'H' and (resid 1 through 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 119 )HA34 - 11934 - 119
33chain 'H' and (resid 120 through 143 )HA120 - 143120 - 137
44chain 'H' and (resid 144 through 162 )HA144 - 162138 - 156
55chain 'H' and (resid 163 through 201 )HA163 - 201157 - 195
66chain 'H' and (resid 202 through 221 )HA202 - 221196 - 215
77chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
88chain 'L' and (resid 19 through 38 )LB19 - 3819 - 38
99chain 'L' and (resid 39 through 119 )LB39 - 11939 - 119
1010chain 'L' and (resid 120 through 140 )LB120 - 140120 - 140
1111chain 'L' and (resid 141 through 151 )LB141 - 151141 - 151
1212chain 'L' and (resid 152 through 164 )LB152 - 164152 - 164
1313chain 'L' and (resid 165 through 183 )LB165 - 183165 - 183
1414chain 'L' and (resid 184 through 199 )LB184 - 199184 - 199
1515chain 'L' and (resid 200 through 212 )LB200 - 212200 - 212
1616chain 'E' and (resid 334 through 364 )EC334 - 3641 - 31
1717chain 'E' and (resid 365 through 375 )EC365 - 37532 - 42
1818chain 'E' and (resid 376 through 442 )EC376 - 44243 - 109
1919chain 'E' and (resid 443 through 506 )EC443 - 506110 - 173
2020chain 'E' and (resid 507 through 527 )EC507 - 527174 - 194
2121chain 'A' and (resid 1 through 17 )AH1 - 171 - 17
2222chain 'A' and (resid 18 through 125 )AH18 - 12518 - 125
2323chain 'A' and (resid 126 through 220 )AH126 - 220126 - 215
2424chain 'B' and (resid 1 through 18 )BL1 - 181 - 18
2525chain 'B' and (resid 19 through 30 )BL19 - 3019 - 30
2626chain 'B' and (resid 31 through 76 )BL31 - 7631 - 76
2727chain 'B' and (resid 77 through 98 )BL77 - 9877 - 98
2828chain 'B' and (resid 99 through 137 )BL99 - 13799 - 137
2929chain 'B' and (resid 138 through 150 )BL138 - 150138 - 150
3030chain 'B' and (resid 151 through 163 )BL151 - 163151 - 163
3131chain 'B' and (resid 164 through 198 )BL164 - 198164 - 198
3232chain 'B' and (resid 199 through 213 )BL199 - 213199 - 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://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