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- PDB-7pr0: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

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基本情報

登録情報
データベース: PDB / ID: 7pr0
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab
要素
  • FD-5D Fab heavy chain
  • FD-5D Fab light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 antibody / receptor-binding-domain / RBD / spike / neutralisation / FI-3A / FD-11A / FD-5D / 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 / 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 / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
類似検索 - ドメイン・相同性
NITRATE ION / Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.92 Å
データ登録者Zhou, D. / Ren, J. / Stuart, D.I.
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: Theranostics / 年: 2022
タイトル: Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
著者: Kuan-Ying A Huang / Daming Zhou / Tiong Kit Tan / Charles Chen / Helen M E Duyvesteyn / Yuguang Zhao / Helen M Ginn / Ling Qin / Pramila Rijal / Lisa Schimanski / Robert Donat / Adam Harding ...著者: Kuan-Ying A Huang / Daming Zhou / Tiong Kit Tan / Charles Chen / Helen M E Duyvesteyn / Yuguang Zhao / Helen M Ginn / Ling Qin / Pramila Rijal / Lisa Schimanski / Robert Donat / Adam Harding / Javier Gilbert-Jaramillo / William James / Julia A Tree / Karen Buttigieg / Miles Carroll / Sue Charlton / Chia-En Lien / Meei-Yun Lin / Cheng-Pin Chen / Shu-Hsing Cheng / Xiaorui Chen / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Che Ma / Alain R Townsend / David I Stuart /
要旨: Administration of potent anti-receptor-binding domain (RBD) monoclonal antibodies has been shown to curtail viral shedding and reduce hospitalization in patients with SARS-CoV-2 infection. However, ... Administration of potent anti-receptor-binding domain (RBD) monoclonal antibodies has been shown to curtail viral shedding and reduce hospitalization in patients with SARS-CoV-2 infection. However, the structure-function analysis of potent human anti-RBD monoclonal antibodies and its links to the formulation of antibody cocktails remains largely elusive. Previously, we isolated a panel of neutralizing anti-RBD monoclonal antibodies from convalescent patients and showed their neutralization efficacy . Here, we elucidate the mechanism of action of antibodies and dissect antibodies at the epitope level, which leads to a formation of a potent antibody cocktail. We found that representative antibodies which target non-overlapping epitopes are effective against wild type virus and recently emerging variants of concern, whilst being encoded by antibody genes with few somatic mutations. Neutralization is associated with the inhibition of binding of viral RBD to ACE2 and possibly of the subsequent fusion process. Structural analysis of representative antibodies, by cryo-electron microscopy and crystallography, reveals that they have some unique aspects that are of potential value while sharing some features in common with previously reported neutralizing monoclonal antibodies. For instance, one has a common VH 3-53 public variable region yet is unusually resilient to mutation at residue 501 of the RBD. We evaluate the efficacy of an antibody cocktail consisting of two potent non-competing anti-RBD antibodies in a Syrian hamster model. We demonstrate that the cocktail prevents weight loss, reduces lung viral load and attenuates pulmonary inflammation in hamsters in both prophylactic and therapeutic settings. Although neutralization of one of these antibodies is abrogated by the mutations of variant B.1.351, it is also possible to produce a bi-valent cocktail of antibodies both of which are resilient to variants B.1.1.7, B.1.351 and B.1.617.2. These findings support the up-to-date and rational design of an anti-RBD antibody cocktail as a therapeutic candidate against COVID-19.
履歴
登録2021年9月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年2月2日Provider: repository / タイプ: Initial release
改定 1.12024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

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集合体

登録構造単位
E: Spike protein S1
L: FD-5D Fab light chain
H: FD-5D Fab heavy chain
A: Spike protein S1
B: FD-5D Fab light chain
C: FD-5D Fab heavy chain
D: Spike protein S1
F: FD-5D Fab light chain
G: FD-5D Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)217,06023
ポリマ－215,6329
非ポリマー1,42814
水00
1
E: Spike protein S1
L: FD-5D Fab light chain
H: FD-5D Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,58211
ポリマ－71,8773
非ポリマー7048
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Spike protein S1
B: FD-5D Fab light chain
C: FD-5D Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,2536
ポリマ－71,8773
非ポリマー3753
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
D: Spike protein S1
F: FD-5D Fab light chain
G: FD-5D Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,2266
ポリマ－71,8773
非ポリマー3493
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)231.308, 146.064, 78.578
Angle α, β, γ (deg.)90.000, 103.680, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and ((resid 329 and (name N or name...
d_2ens_1(chain "D" and (resid 329 through 339 or resid 341...
d_3ens_1(chain "E" and (resid 329 through 339 or resid 341...
d_1ens_2(chain "B" and (resid 1 through 23 or resid 25...
d_2ens_2(chain "F" and (resid 1 through 23 or resid 25...
d_3ens_2(chain "L" and (resid 1 through 23 or resid 25...
d_1ens_3(chain "C" and (resid 2 through 120 or resid 122...
d_2ens_3(chain "H" and (resid 2 through 120 or resid 122...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISGLYG2 - 12
d_12ens_1VALVALG14 - 80
d_13ens_1GLNLEUG82 - 134
d_14ens_1PROGLYG136 - 158
d_15ens_1ASNCYSG160 - 198
d_21ens_1HISGLYM1 - 11
d_22ens_1VALVALM13 - 79
d_23ens_1GLNLEUM81 - 133
d_24ens_1PROGLYM135 - 157
d_25ens_1ASNCYSM159 - 197
d_31ens_1HISGLYA1 - 11
d_32ens_1VALVALA13 - 79
d_33ens_1GLNLEUA81 - 133
d_34ens_1PROGLYA135 - 157
d_35ens_1ASNCYSA159 - 197
d_11ens_2ASPCYSI1 - 23
d_12ens_2SERGLYI25 - 106
d_13ens_2GLYILEI108 - 124
d_14ens_2PROASPI126 - 129
d_15ens_2GLNARGI131 - 149
d_16ens_2ALASERI151 - 175
d_17ens_2ASPHISI177 - 196
d_18ens_2VALASNI198 - 217
d_21ens_2ASPCYSO1 - 23
d_22ens_2SERGLYO25 - 106
d_23ens_2GLYILEO108 - 124
d_24ens_2PROASPO126 - 129
d_25ens_2GLNARGO131 - 149
d_26ens_2ALASERO151 - 175
d_27ens_2ASPHISO177 - 196
d_28ens_2VALASNO198 - 217
d_31ens_2ASPCYSC1 - 23
d_32ens_2SERGLYC25 - 106
d_33ens_2GLYILEC108 - 124
d_34ens_2PROASPC126 - 129
d_35ens_2GLNARGC131 - 149
d_36ens_2ALASERC151 - 175
d_37ens_2ASPHISC177 - 196
d_38ens_2VALASNC198 - 217
d_11ens_3VALGLYK1 - 119
d_12ens_3GLYLYSK121 - 219
d_13ens_3VALPROK221 - 223
d_14ens_3NO3NO3L
d_21ens_3VALGLYE1 - 119
d_22ens_3GLYSERE121 - 143
d_23ens_3GLYLYSE149 - 224
d_24ens_3VALPROE226 - 228
d_25ens_3NO3NO3F

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.517021319305, -0.389051163868, 0.76244878338), (0.619657718634, 0.444387908813, 0.646949532992), (-0.590519489197, 0.806943974755, 0.0113205337367)-71.0838227528, 74.4003681667, -89.0329147731
2given(-0.454496182575, 0.598093280289, -0.66008912133), (-0.427125230111, 0.50396352939, 0.750722850889), (0.781663135774, 0.623141387743, 0.0264112297071)-131.931080547, 4.61292001927, 9.65714353643
3given(-0.579041884419, -0.277190657646, 0.766730614624), (0.633912966508, 0.438325024731, 0.637201321081), (-0.512703468861, 0.855006732142, -0.0780937962312)-82.3583265609, 74.6614615432, -91.6059285096
4given(-0.39849436406, 0.590015974014, -0.702198969111), (-0.387328184632, 0.585733814679, 0.711964026992), (0.83137182969, 0.555695104126, -0.00488180786978)-129.618324935, -0.567236759011, 15.9929129835
5given(-0.405311359985, 0.612632211226, -0.678531115893), (-0.384490947507, 0.559151830791, 0.734517488838), (0.829390989071, 0.558597353996, 0.00892095039175)-130.749617841, 2.81356039806, 16.5954610947

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要素

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抗体 , 2種, 6分子 LBFHCG

#2: 抗体 FD-5D Fab light chain


分子量: 24189.945 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: Homo sapiens (ヒト)
#3: 抗体 FD-5D Fab heavy chain


分子量: 24536.383 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: Homo sapiens (ヒト)

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タンパク質 / 糖 , 2種, 6分子 EAD

#1: タンパク質 Spike protein S1


分子量: 23150.891 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
#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: 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 , 4種, 11分子

#5: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / 式: SO4
#6: 化合物 ChemComp-NO3 / NITRATE ION


分子量: 62.005 Da / 分子数: 3 / 由来タイプ: 合成 / 式: NO3
#7: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Cl
#8: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3

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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: 2.99 Å3/Da / 溶媒含有率: 58.87 %
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: 10% (w/v) PEG 20 000, 20% (v/v) PEG MME 550, 0.03 M of each NPS (NaNO3; Na2HPO4; (NH4)2SO4) and 0.1 M bicine/Trizma base pH 8.5.

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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: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年7月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97625 Å / 相対比: 1
反射解像度: 2.92→73 Å / Num. obs: 54960 / % possible obs: 99.8 % / 冗長度: 16.6 % / Biso Wilson estimate: 104.99 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.072 / Net I/σ(I): 5.7
反射 シェル解像度: 2.92→2.97 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2589 / CC1/2: 0.341 / % possible all: 95.6

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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: 7PQZ

7pqz


解像度: 2.92→71.5 Å / SU ML: 0.548 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 33.6018
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2506 2524 4.96 %
Rwork0.2136 48404 -
obs0.2154 50928 92.47 %
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: 125.74 Å2
精密化ステップサイクル: LAST / 解像度: 2.92→71.5 Å
タンパク質核酸リガンド溶媒全体
原子数14508 0 84 0 14592
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003414946
X-RAY DIFFRACTIONf_angle_d0.635120342
X-RAY DIFFRACTIONf_chiral_restr0.04522250
X-RAY DIFFRACTIONf_plane_restr0.00482617
X-RAY DIFFRACTIONf_dihedral_angle_d11.61535278
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.701129452934
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.655537785661
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.976712366934
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.869654298697
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.661447794193
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.980.5636270.545431X-RAY DIFFRACTION15.2
2.98-3.040.4207830.50131576X-RAY DIFFRACTION54.2
3.04-3.10.44911390.44412756X-RAY DIFFRACTION95.32
3.1-3.170.44561660.4082895X-RAY DIFFRACTION99.9
3.17-3.250.39211420.38452915X-RAY DIFFRACTION99.97
3.25-3.340.33211480.34452874X-RAY DIFFRACTION99.9
3.34-3.440.37831610.31882895X-RAY DIFFRACTION99.9
3.44-3.550.34061420.28722885X-RAY DIFFRACTION99.9
3.55-3.680.33291360.27812930X-RAY DIFFRACTION99.8
3.68-3.830.28921360.25032894X-RAY DIFFRACTION100
3.83-40.26561540.22212909X-RAY DIFFRACTION99.93
4-4.210.2351560.1992910X-RAY DIFFRACTION100
4.21-4.470.21721350.17582924X-RAY DIFFRACTION100
4.47-4.820.19851590.1622883X-RAY DIFFRACTION99.93
4.82-5.30.20271630.16822926X-RAY DIFFRACTION100
5.31-6.070.24721520.18092923X-RAY DIFFRACTION100
6.07-7.650.22391630.19442917X-RAY DIFFRACTION100
7.65-71.50.19671620.16312961X-RAY DIFFRACTION99.43
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)
13.89176195829-0.234366257224-0.5566938307355.7885806746-1.118163383993.170561818460.7754958983911.58556663849-0.9134713662970.705256989287-0.435159814404-1.081483838932.245471838551.12393355314-0.09509487698091.85966673050.527424553059-0.3690245028981.16984188985-0.2159165407211.25376097972-80.034738324121.043863912526.9474827893
20.6661356949461.757270452981.502514531746.607049100034.920492327893.58892758795-0.3875559105641.57722669027-1.68237075797-2.759152733571.224496989-0.9072208080341.264605079272.88439494159-0.6605947302442.854088693420.4422291221660.1459354798791.81410653776-0.4062097285321.63082858038-88.063608445314.877872759121.7373659368
34.19163964942-0.446940282713-0.8044402229781.84579563322-2.988287599586.03987653325-1.858188299851.20090789436-0.37126881626-0.1431388519240.72049350169-0.5569329325661.311146931042.148845408281.218037481991.399467097650.04756244021190.04076572477091.68644210755-0.2902822297421.33114599462-79.946031907817.617085804824.5736481503
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522.68085037745-1.118795938071.210038290442.49023573114-0.3485061389415.17316257738-0.111592523144-0.6235446558140.399918548696-0.5872185301430.0835742129676-0.0179703087069-0.844564923449-0.588248536380.1158063304541.14553504194-0.0185250756014-0.1327501539191.012759630210.008434586292280.611903158993-87.257857909847.1607491844-17.9982459251
534.261815784961.643940537563.288014855722.561165329861.710588025624.47275229379-0.504064578384-1.15634531895-1.12663978141-0.4716958665950.1417751721390.264714671325-0.259683429957-2.94107850175-0.02357401234290.80996839217-0.4530368199720.03284153090353.340584592420.2662227360441.2943932807-110.0964582435.256191012216.2092852009
540.820862064601-0.681305523588-1.311737368886.6743103993-2.226969882164.04977993685-0.4534818529790.3488443429940.355076536663-0.3260617738420.6143394977490.384916670159-0.563786326163-2.579584409140.119539657580.7773864124950.304025087642-0.1032980851782.69841941362-0.1774493006141.04394084919-107.43589460344.23851344548.76607413325
555.406865967643.308506276690.7340285018429.7486121215-0.5293353563753.99647826638-0.0288569938407-0.512172922388-0.2053250867060.478647089860.1870834575160.4962803131950.613838421221-1.91099116276-0.8746395754910.841902214947-0.174594423266-0.001024093297312.00100198042-0.0834653920590.825910005296-104.57341482135.593826313713.9020625861
560.4048495196770.06212149703520.1605797955144.85580320875-0.2875359368826.13703265580.641997504968-0.99123061466-1.180381716660.7742282460470.28517502579-0.0660870352731.21087764433-1.87815940012-0.928949934411.63211295623-0.38393252072-0.4850233899021.531950136750.3120057668791.57678505075-95.37015269715.347142674232.6745619199
571.02367299994-0.0718576544937-0.879529516492-0.101806564415-0.09820615135290.756781141344-0.2866991239511.688009296080.84398051910.752216690699-0.530557825136-0.3560863650730.0308870363254-1.34806722542-1.528501301131.50563555744-2.443979044090.1360027128450.365502443743.381291082641.35638437768-102.74971612510.709403273637.9910338107
581.175793118770.805305749395-1.061443039311.88079535791.338411815143.81129556590.245036440579-0.119868859472-0.58584347309-0.433227041649-0.0391990792628-0.4691277976490.891284160501-0.2009123273190.6079499694610.8262833571160.1037668671470.1131003382381.145133210460.083716713860.822371075135-80.113768819840.448273542915.1757277011
592.31791477297-1.694972774763.489892059833.93967624137-0.2601323284079.1519974206-0.179408037466-0.3145976757380.1866806144740.0165967969594-0.2562779247030.222556698263-1.21435454621-0.4723410534090.3134160569970.8416403373620.242214561095-0.02536088805811.37349056369-0.1531930492330.721300928574-86.447303575350.549961910214.2428904392
601.74302278402-1.904884955650.5496488289561.29159330994-0.3923902126973.74440110402-0.331237613029-0.322601265828-0.05782688569870.263964235093-0.1603198320750.0193335163796-0.887366552564-0.1187628089960.5252330703120.9222296861040.113811820688-0.02870340539171.52487226969-0.07497880698890.752001860054-86.285021913349.407559921916.070791257
615.50413943101-1.467946569673.409875048774.63301427841-2.924039814886.00515854220.1792788541080.600680747763-1.01588213677-0.3686016833690.2642025009721.32536380622-0.316584787441-1.23941379588-0.536738762780.7768861286470.3040922379180.02428488726381.541522494110.09222999777870.733523101935-93.10939242246.70158721548.21415410829
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 'G' and (resid 126 through 170 )GQ126 - 170126 - 153
22chain 'G' and (resid 171 through 188 )GQ171 - 188154 - 171
33chain 'G' and (resid 189 through 221 )GQ189 - 221172 - 191
44chain 'E' and (resid 329 through 349 )EA329 - 3491 - 21
55chain 'E' and (resid 350 through 370 )EA350 - 37022 - 42
66chain 'E' and (resid 371 through 409 )EA371 - 40943 - 81
77chain 'E' and (resid 410 through 421 )EA410 - 42182 - 93
88chain 'E' and (resid 422 through 469 )EA422 - 46994 - 141
99chain 'E' and (resid 470 through 479 )EA470 - 479142 - 151
1010chain 'E' and (resid 480 through 494 )EA480 - 494152 - 166
1111chain 'E' and (resid 495 through 506 )EA495 - 506167 - 178
1212chain 'E' and (resid 507 through 525 )EA507 - 525179 - 197
1313chain 'L' and (resid 1 through 18 )LC1 - 181 - 18
1414chain 'L' and (resid 19 through 37 )LC19 - 3719 - 37
1515chain 'L' and (resid 38 through 53 )LC38 - 5338 - 53
1616chain 'L' and (resid 54 through 66 )LC54 - 6654 - 66
1717chain 'L' and (resid 67 through 80 )LC67 - 8067 - 80
1818chain 'L' and (resid 81 through 95 )LC81 - 9581 - 95
1919chain 'L' and (resid 96 through 120 )LC96 - 12096 - 120
2020chain 'L' and (resid 121 through 157 )LC121 - 157121 - 157
2121chain 'L' and (resid 158 through 170 )LC158 - 170158 - 170
2222chain 'L' and (resid 171 through 194 )LC171 - 194171 - 194
2323chain 'L' and (resid 195 through 205 )LC195 - 205195 - 205
2424chain 'L' and (resid 206 through 221 )LC206 - 221206 - 221
2525chain 'H' and (resid 2 through 135 )HE2 - 1351 - 134
2626chain 'H' and (resid 136 through 150 )HE136 - 150135 - 149
2727chain 'H' and (resid 151 through 229 )HE151 - 229150 - 228
2828chain 'A' and (resid 328 through 349 )AG328 - 3491 - 22
2929chain 'A' and (resid 350 through 375 )AG350 - 37523 - 48
3030chain 'A' and (resid 376 through 469 )AG376 - 46949 - 142
3131chain 'A' and (resid 470 through 526 )AG470 - 526143 - 199
3232chain 'B' and (resid 1 through 18 )BI1 - 181 - 18
3333chain 'B' and (resid 19 through 37 )BI19 - 3719 - 37
3434chain 'B' and (resid 38 through 66 )BI38 - 6638 - 66
3535chain 'B' and (resid 67 through 120 )BI67 - 12067 - 120
3636chain 'B' and (resid 121 through 135 )BI121 - 135121 - 135
3737chain 'B' and (resid 136 through 181 )BI136 - 181136 - 181
3838chain 'B' and (resid 182 through 219 )BI182 - 219182 - 219
3939chain 'C' and (resid 2 through 44 )CK2 - 441 - 43
4040chain 'C' and (resid 45 through 76 )CK45 - 7644 - 75
4141chain 'C' and (resid 77 through 109 )CK77 - 10976 - 108
4242chain 'C' and (resid 110 through 161 )CK110 - 161109 - 155
4343chain 'C' and (resid 162 through 204 )CK162 - 204156 - 198
4444chain 'C' and (resid 205 through 229 )CK205 - 229199 - 223
4545chain 'D' and (resid 329 through 349 )DM329 - 3491 - 21
4646chain 'D' and (resid 350 through 364 )DM350 - 36422 - 36
4747chain 'D' and (resid 365 through 375 )DM365 - 37537 - 47
4848chain 'D' and (resid 376 through 421 )DM376 - 42148 - 93
4949chain 'D' and (resid 422 through 459 )DM422 - 45994 - 131
5050chain 'D' and (resid 460 through 479 )DM460 - 479132 - 151
5151chain 'D' and (resid 480 through 494 )DM480 - 494152 - 166
5252chain 'D' and (resid 495 through 525 )DM495 - 525167 - 197
5353chain 'F' and (resid 1 through 18 )FO1 - 181 - 18
5454chain 'F' and (resid 19 through 80 )FO19 - 8019 - 80
5555chain 'F' and (resid 81 through 120 )FO81 - 12081 - 120
5656chain 'F' and (resid 121 through 194 )FO121 - 194121 - 194
5757chain 'F' and (resid 195 through 217 )FO195 - 217195 - 217
5858chain 'G' and (resid 1 through 17 )GQ1 - 171 - 17
5959chain 'G' and (resid 18 through 76 )GQ18 - 7618 - 76
6060chain 'G' and (resid 77 through 109 )GQ77 - 10977 - 109
6161chain 'G' and (resid 110 through 125 )GQ110 - 125110 - 125

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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