[日本語] English
万見
- PDB-8smt: Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8smt
タイトルCrystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain
要素
  • (WRAIR-2134 Fab ...) x 2
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / antibody / sars-cov-2 / immune system / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / 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 / 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: 3.16 Å
データ登録者Sankhala, R.S. / Jensen, J.L. / Joyce, M.G.
資金援助 米国, 1件
組織認可番号国
Department of Defense (DOD, United States)W81XWH-18-2-0040 米国
引用ジャーナル: Structure / 年: 2024
タイトル: Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
著者: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, C. ...著者: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, C. / Soman, S. / King, J. / Corbitt, C. / Zemil, M. / Peterson, C.E. / Mendez-Rivera, L. / Townsley, S.M. / Donofrio, G.C. / Lal, K.G. / Tran, U. / Green, E.C. / Smith, C. / de Val, N. / Laing, E.D. / Broder, C.C. / Currier, J.R. / Gromowski, G.D. / Wieczorek, L. / Rolland, M. / Paquin-Proulx, D. / van Dyk, D. / Britton, Z. / Rajan, S. / Loo, Y.M. / McTamney, P.M. / Esser, M.T. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Modjarrad, K. / Joyce, M.G.
履歴
登録2023年4月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年6月28日Provider: repository / タイプ: Initial release
改定 1.12024年1月10日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年2月14日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

-
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

-
集合体

登録構造単位
A: WRAIR-2134 Fab heavy chain
B: WRAIR-2134 Fab light chain
D: WRAIR-2134 Fab heavy chain
F: WRAIR-2134 Fab light chain
H: WRAIR-2134 Fab heavy chain
I: WRAIR-2134 Fab heavy chain
J: WRAIR-2134 Fab light chain
L: WRAIR-2134 Fab light chain
C: Spike protein S1
E: Spike protein S1
G: Spike protein S1
K: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)284,87316
ポリマ－283,29912
非ポリマー1,5744
水00
1
A: WRAIR-2134 Fab heavy chain
B: WRAIR-2134 Fab light chain
C: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,0464
ポリマ－70,8253
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: WRAIR-2134 Fab heavy chain
F: WRAIR-2134 Fab light chain
G: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,3704
ポリマ－70,8253
非ポリマー5451
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
H: WRAIR-2134 Fab heavy chain
L: WRAIR-2134 Fab light chain
E: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,0464
ポリマ－70,8253
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
I: WRAIR-2134 Fab heavy chain
J: WRAIR-2134 Fab light chain
K: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,4114
ポリマ－70,8253
非ポリマー5871
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)143.190, 154.430, 165.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
要素

-
タンパク質 , 1種, 4分子 CEGK

#3: タンパク質
Spike protein S1


分子量: 23073.766 Da / 分子数: 4 / Fragment: receptor binding domain / 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 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2

-
抗体 , 2種, 8分子 ADHIBFJL

#1: 抗体
WRAIR-2134 Fab heavy chain


分子量: 24941.795 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体
WRAIR-2134 Fab light chain


分子量: 22809.164 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)

-
糖 , 3種, 4分子

#4: 多糖 beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 545.490 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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: 2 / 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

-
詳細

研究の焦点であるリガンドがあるかN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.28 Å3/Da / 溶媒含有率: 62.55 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350

-
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: APS / ビームライン: 24-ID-E / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年6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: 0.9792 Å / 相対比: 1
反射解像度: 3.15→50 Å / Num. obs: 63643 / % possible obs: 99.7 % / 冗長度: 6.8 % / CC1/2: 0.993 / Rrim(I) all: 0.176 / Net I/σ(I): 7.15
反射 シェル解像度: 3.15→3.34 Å / Num. unique obs: 19496 / CC1/2: 0.428 / Rrim(I) all: 1.691

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
HKL-2000データ削減
HKL-2000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 / 解像度: 3.16→49.147 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 24.5 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2486 2985 5.06 %
Rwork0.2144 --
obs0.2161 58948 92.95 %
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
精密化ステップサイクル: LAST / 解像度: 3.16→49.147 Å
タンパク質核酸リガンド溶媒全体
原子数19573 0 103 0 19676
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00620262
X-RAY DIFFRACTIONf_angle_d0.98327658
X-RAY DIFFRACTIONf_dihedral_angle_d13.6437266
X-RAY DIFFRACTIONf_chiral_restr0.0663019
X-RAY DIFFRACTIONf_plane_restr0.0073546
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.21130.3556250.3012406X-RAY DIFFRACTION14
3.2113-3.26670.2573850.30611418X-RAY DIFFRACTION50
3.2667-3.32610.31831420.31262440X-RAY DIFFRACTION87
3.3261-3.39010.36821390.30432842X-RAY DIFFRACTION100
3.3901-3.45920.35981440.27692830X-RAY DIFFRACTION100
3.4592-3.53440.32021470.26472860X-RAY DIFFRACTION100
3.5344-3.61660.30171310.25832837X-RAY DIFFRACTION100
3.6166-3.7070.29281690.25972850X-RAY DIFFRACTION100
3.707-3.80720.31641410.2492812X-RAY DIFFRACTION100
3.8072-3.91920.23131640.22992842X-RAY DIFFRACTION100
3.9192-4.04570.25041570.21212859X-RAY DIFFRACTION100
4.0457-4.19020.22781480.20322856X-RAY DIFFRACTION100
4.1902-4.35790.20161620.18342831X-RAY DIFFRACTION100
4.3579-4.55610.23091640.1792863X-RAY DIFFRACTION100
4.5561-4.79610.19791230.17532878X-RAY DIFFRACTION100
4.7961-5.09630.20661550.17462865X-RAY DIFFRACTION100
5.0963-5.48930.21291590.1852876X-RAY DIFFRACTION100
5.4893-6.04080.25061610.21142886X-RAY DIFFRACTION100
6.0408-6.91290.2221530.22112912X-RAY DIFFRACTION100
6.9129-8.70160.26951620.19572946X-RAY DIFFRACTION100
8.7016-49.1470.22241540.20043054X-RAY DIFFRACTION99
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)
12.85312.4659-0.59323.7132-0.48791.5471-0.27920.10290.42-0.12830.30480.2147-0.0784-0.24620.08690.51610.0994-0.12620.4598-0.01150.5743-4.728-48.67211.489
21.6525-0.35-2.17066.376-0.06372.705-0.0785-2.17151.36831.6224-0.2925-1.2964-0.9191-0.17060.10711.1545-0.0437-0.32521.0139-0.38781.309427.632-20.7725.053
33.09411.3556-0.58843.7764-0.07132.0963-0.0203-0.41990.6374-0.33090.129-0.2791-0.33190.1349-0.02580.74730.1124-0.18110.4707-0.11931.015320.771-24.49314.519
45.50190.5258-0.65184.8098-0.42672.4550.1758-0.89660.1521.1705-0.4086-0.2304-0.081-0.0027-0.03530.81740.1135-0.17580.8213-0.19780.50368.421-53.46834.276
52.24951.72560.88994.774-0.57652.66060.0633-0.3842-0.33950.6749-0.1069-0.38350.34310.3787-0.02070.80880.1195-0.15850.5912-0.01760.57516.06-59.87726.82
65.76341.63710.08194.9198-0.09063.34470.477-0.47010.23360.44980.03750.04740.1955-1.9508-0.16840.84650.06070.04571.06610.10010.5099-8.568-55.39425.045
72.12982.1548-0.03164.2227-0.86451.46910.3727-0.65450.42481.1035-0.1131-0.3318-0.70450.1506-0.0211.13160.0711-0.17120.7499-0.23130.875218.877-28.32329.812
82.20841.66410.27223.88770.04962.1750.0046-0.96590.72531.4234-0.08370.2337-0.7152-0.0293-0.05361.3043-0.0001-0.09580.9624-0.28820.933916.513-23.21733.16
92.89230.5215-0.80444.02720.32452.4531-0.21860.0571-0.2668-0.03870.1459-0.37920.1680.35910.01340.440.047-0.02870.38590.03330.4475-19.526-9.3576.402
101.65270.35080.19743.10270.98420.9698-0.1333-0.1834-0.1686-0.08080.0846-0.11470.02710.18340.06580.5039-0.0317-0.01830.45260.07580.4698-23.336-6.21611.221
112.3289-0.27022.30823.9579-0.72852.23450.125-1.61150.54840.57660.38130.31450.0724-1.03660.2450.7211-0.1981-0.17891.2307-0.06770.8042-39.31622.85634.635
121.29580.2559-0.14112.49190.00283.34150.071-0.90160.73770.4882-0.1992-0.2973-0.4630.31070.04970.5738-0.095-0.22050.8709-0.12770.7093-27.77621.94729.609
132.9443-0.3177-1.393.48140.68422-0.0626-0.3323-0.38960.1954-0.1714-0.33370.32790.04750.23590.51160.0683-0.04020.41970.13680.5041-34.011-17.67523.556
146.50750.20380.06276.3944-0.0277.0032-0.40791.4588-0.7592-1.42490.18480.018-0.0948-0.61330.34110.6991-0.12650.04130.66510.02530.7118-35.677-14.6988.044
151.262-1.0847-0.20653.0384-0.1638-0.0283-0.7017-1.05960.53811.1762-0.3611-0.61820.6401-0.1220.1030.517-0.0042-0.27150.92830.12820.2208-38.9842.05335.01
163.19670.1064-0.71324.5504-0.89212.24950.0004-0.2090.30230.29890.0008-0.0421-0.15720.15010.04360.51530.0158-0.15660.4419-0.07950.4773-42.71214.49725.009
173.1137-1.5166-0.85884.1320.36112.6718-0.0624-0.0176-0.21350.2036-0.13280.44330.281-0.15690.20610.3631-0.04190.02180.33970.02380.3997-48.531-28.47672.537
183.0998-2.02160.24013.72080.51970.7347-0.25560.13180.08440.15740.040.39880.1745-0.07480.14340.663-0.06760.01510.37530.05660.3023-43.317-28.93869.011
193.51861.20812.16147.43210.36181.3033-0.09941.584-1.189-1.7870.6974-0.37680.0132-0.04030.06291.04710.02220.33530.7581-0.21310.5912-17.188-56.05853.063
203.9465-0.8206-0.29143.57980.19051.9313-0.00770.3896-0.29550.11040.1181-0.20920.51350.1770.00490.6376-0.03310.02250.4541-0.08440.507-22.804-52.91763.932
212.298-0.1410.88824.8883-1.18382.2656-0.04150.1385-0.0637-0.342-0.01930.41180.2156-0.1425-0.030.4460.1047-0.03260.4182-0.05470.5291-82.90710.4952.693
222.0525-0.16140.09084.2102-1.52860.90120.08540.0083-0.1224-0.2722-0.10680.42180.079-0.0846-0.01040.50870.03020.0220.4572-0.09220.382-79.3127.4548.264
232.7464-1.3743-2.72935.37320.36822.720.1907-1.3696-0.44351.3614-0.0831-0.593-0.190.51470.04240.9847-0.28980.02041.15940.24321.0114-65.086-20.72435.99
241.3366-0.69160.97173.5299-0.82173.0188-0.0548-1.0498-0.9230.74250.06670.74440.2502-0.5864-0.26940.6791-0.14350.21241.06130.14460.9478-76.373-20.23330.282
253.7394-0.15780.44444.4298-2.19831.15210.0387-0.281-0.33570.5629-0.1465-0.2182-0.23620.31110.10480.3830.1609-0.02720.5592-0.01120.4621-63.71514.53723.05
262.9041-0.20371.23523.8527-0.58222.1286-0.0231-0.10380.43830.48120.05030.4608-0.1777-0.06270.0790.4330.070.01240.3773-0.06260.4688-70.41720.8519.598
276.9967-0.9071.05665.27320.90662.0496-0.10880.86940.1434-1.1462-0.0652-0.2048-0.0750.69050.19430.5742-0.00840.00550.5221-0.08970.5448-67.04315.3626.423
282.4012-0.3061-0.58054.822-0.63231.9787-0.2521-0.2163-0.66690.17240.180.29780.2657-0.36820.00670.4102-0.00980.02630.53750.09520.5847-63.279-10.67526.268
294.1846-0.3941-0.08335.94881.18093.7925-0.3229-0.2375-0.59071.52530.7453-0.62240.4930.35160.0370.67270.13730.03220.59250.090.6418-55.721-10.62829.511
303.3925-0.7630.44954.82580.10322.58810.09580.7740.1984-0.2604-0.39370.1403-0.07640.09320.07710.7565-0.064-0.07910.88230.20570.3714-38.106-23.63347.041
313.4534-3.4065-1.19765.23541.29573.7108-0.17620.77041.5581-0.3467-1.96283.0132-0.4525-1.37970.1421.02120.3278-0.05620.82490.51720.035-48.259-16.31450.227
320.8807-0.7012-0.1093.86440.20532.0547-0.22630.16290.3040.1455-0.0057-0.0714-0.1807-0.22820.14220.49790.020.1120.48870.19240.5652-36.393-22.15160.002
331.9543-1.6550.28093.93680.44373.0638-0.47570.16310.9358-0.6594-0.0971-0.1956-0.5297-0.08990.15630.7359-0.07890.00240.73330.37660.6381-38.034-12.23654.194
343.1083-1.7051-0.3663.09620.08011.9258-0.26780.65810.5448-0.34560.09240.04840.0876-0.2240.05460.7006-0.0673-0.1330.62570.2760.5013-41.991-21.25156.576
352.3527-1.84380.04553.91780.45481.2660.26440.5472-0.2472-0.15-0.228-0.02620.3903-0.08250.07160.8483-0.0910.07930.6764-0.06180.4649-25.82-49.13150.939
362.114-1.44430.28353.0173-0.26382.3481-0.0020.97820.0386-0.99280.18530.12340.70970.06340.04381.0021-0.0334-0.0190.8521-0.08880.5686-27.628-48.28346.756
370.814-0.16670.88944.92582.06132.03691.08721.68620.0375-0.9926-0.48651.00861.072-0.20370.14161.57040.0454-0.29861.42230.02560.7782-36.767-56.3943.676
383.0205-1.6423-0.02151.8492-0.4142.36730.07030.18710.2859-0.0674-0.0899-0.07350.0848-0.3280.070.94130.04360.04890.73350.10150.6313-26.681-44.16652.616
391.227-1.2595-0.14393.50810.07721.35280.11440.9296-0.3595-0.7802-0.48090.45511.3393-0.2970.09241.5944-0.3525-0.0351.1327-0.30280.6862-30.636-61.41244.248
402.1558-0.2315-0.17914.38530.27922.2570.25121.0702-0.4394-1.3495-0.4368-0.11720.66430.12490.07761.337-0.09450.17811.1027-0.1230.7788-23.976-55.34940.955
416.55070.13350.89424.20310.74072.93530.76610.5598-0.57490.9266-0.57691.0297-0.3489-0.211-0.13460.7565-0.130.16990.6371-0.06360.8756-28.7-76.00711.136
424.60170.0282.03926.0797-0.77264.1018-0.15660.1491-0.58180.92520.30750.7213-0.0253-0.4395-0.10920.6816-0.03970.20020.63870.03690.8234-23.318-70.11914.414
435.28430.37261.82630.02180.15330.7056-0.4009-0.7384-0.16021.38060.06852.37420.666-1.7732-0.31971.2309-0.2830.47311.0147-0.00221.6923-37.764-75.16621.245
441.88111.85-0.07781.9950.02830.97570.1885-0.94030.23211.9641-0.17281.09820.0387-0.9518-0.07891.1152-0.05990.44251.054-0.15161.2491-33.326-65.82625.597
454.3290.43891.4672.40730.08642.73340.2088-0.8724-1.52232.3214-0.1143-0.27620.2112-0.4533-0.23341.3592-0.17930.09870.7680.1711.0615-18.892-78.66526.658
464.91511.05170.58643.535-0.05972.45740.3544-0.7178-0.50011.8574-0.18291.05030.5406-0.2302-0.17111.2159-0.16550.23160.72210.07140.9247-23.863-77.81524.169
472.62390.6331-1.30574.533-0.7341.98110.41810.0233-2.07161.6208-0.2512-0.86861.0151-0.4575-0.48811.3948-0.1207-0.31040.5103-0.07191.3301-12.71-88.87119.836
484.62520.97530.74722.98040.23272.36770.5686-0.7284-1.95290.9585-0.0252-0.79720.42060.315-0.31431.4055-0.0703-0.32360.5126-0.13021.0166-2.695-79.11823.194
495.26271.3238-0.02354.96430.00754.8328-0.23-0.3656-2.93921.14620.0439-1.0871.78162.3708-0.44151.53340.9376-0.9627-0.57290.14742.27321.628-90.10121.116
504.1191.80030.62152.36310.56952.74930.5759-0.3973-1.6121.6769-0.17470.2580.9039-0.6718-0.29561.1888-0.20690.06720.63090.19071.2979-24.024-85.65722.303
514.84292.43240.71976.6078-0.01295.0209-0.1778-0.99961.17561.46780.19062.1039-0.4451-1.19920.13971.3110.19130.44090.7579-0.00941.5458-32.557-55.23516.556
522.7897-2.2828-0.00674.23220.17762.0578-0.9726-0.80581.28141.76890.80650.761-0.1709-0.08010.01491.26470.29-0.04780.58720.07891.2056-67.165-3.34874.822
535.52951.2241-2.68980.89450.33273.2015-0.5534-0.06560.71741.2040.23522.0044-0.3598-1.2082-0.09691.03830.26470.17130.94060.16451.5405-80.38-1.04568.957
542.0021-2.56870.32365.5322-0.35012.1942-0.11760.39510.7791-0.7873-0.03420.9453-0.3264-0.4830.01090.82840.1434-0.1520.68650.1791.224-71.234-4.6263.627
553.6681-1.57930.26535.2898-0.47712.01510.06661.06741.6783-0.3058-0.1843-0.0126-0.6681-0.42240.04950.9440.2538-0.1830.7910.2621.1084-64.8541.23360.359
561.0925-1.00760.99234.5890.08821.39410.17520.93872.79870.2941-0.4612-1.5512-0.6496-0.20960.02681.00270.0755-0.15210.54720.33612.1474-52.4456.43863.424
570.0848-0.23980.04560.5774-0.11020.03850.56990.73791.6871-0.033-0.0585-2.1059-0.9735-0.15650.10221.7605-0.2774-0.0451.41260.38862.5105-36.58113.62759.04
581.2031-2.1862-0.05533.8124-0.2611.3625-0.44870.6161.7517-0.57150.5766-1.7807-1.68261.14570.05970.65571.1854-0.5979-1.86860.92922.4486-62.0399.9464.523
591.5168-1.9928-0.57915.34990.01492.9017-0.63650.3276-0.59170.38290.19711.5023-0.7534-1.26120.04050.91690.05790.03050.71970.05091.244-74.308-21.12872.609
604.7610.5730.01733.84722.48064.0353-0.31321.07-0.391-0.69990.5177-0.5676-0.43311.4403-0.0820.6986-0.1610.13870.7865-0.17010.7627-20.388-39.948-10.461
613.21130.22371.16054.99630.30246.0713-0.7680.89460.1963-0.81570.45920.1896-0.45910.4138-0.06110.8318-0.2324-0.04020.57530.07660.8517-23.189-32.911-6.164
621.8081-0.03671.47512.33043.24695.7584-0.1481.45550.4503-1.83960.90310.3255-0.85890.331-0.11311.5365-0.17570.20870.9945-0.01850.9452-30.326-40.036-19.582
631.44911.11940.80233.56040.23043.1931-0.14491.0120.603-1.8461-0.47640.5531-1.97430.11160.20361.321-0.1835-0.17170.83080.21981.5223-34.563-30.032-16.779
643.62480.20790.32743.60471.27745.1937-0.24290.0677-0.0035-0.21420.24990.4936-0.2978-0.11030.06270.61260.00620.12170.41440.05820.9235-34.582-40.15-2.657
653.1431.90271.96763.0489-0.24184.76040.3666-0.1098-1.48950.3522-0.0394-0.07820.7006-0.1042-0.1250.81640.0347-0.06120.52960.02791.2263-29.225-49.6286.978
662.5411-0.00851.17064.56830.90654.1758-0.5189-0.98421.21121.20730.27650.24630.379-0.2737-0.02020.87870.20830.15970.5595-0.07350.9068-31.622-38.39315.736
674.10450.7629-0.55186.14270.72155.78430.6029-0.8668-0.97212.09220.0966-0.09261.1007-0.0401-0.21791.26080.01240.00550.74210.18451.136-30.332-49.19821.049
684.02110.94021.03343.64670.9674.9465-0.23750.2369-0.72550.24390.23450.68450.4511-0.0134-0.14440.65550.05520.14780.46490.02941.0971-31.902-48.035-4.441
692.7084-0.3454-0.50325.3404-0.80260.2404-1.25010.51390.7494-0.9936-0.0130.1813-1.4324-0.00790.35631.6952-0.3029-0.2230.93150.1361.4291-26.028-20.03-15.288
704.2663-0.4466-0.49022.9825-1.09715.287-0.71690.91050.4377-0.59420.53990.83890.2915-1.41720.33510.71120.0495-0.14340.61030.06930.864-79.66538.841-16.906
713.79070.591-0.66354.45910.65634.9442-0.61950.46970.0167-0.90710.45310.512-0.2693-0.58240.13820.5469-0.0716-0.060.57030.00960.4444-76.95232.917-11.525
720.41410.3279-0.37680.2515-0.99794.6829-0.99722.15510.055-2.49510.62490.0211-0.0589-0.63490.01331.21460.02170.00071.1469-0.0310.6003-68.73239-24.671
731.25751.4529-0.73692.70950.43161.8795-0.51170.7511-0.835-1.6973-0.2755-0.27961.3450.62490.11671.00510.0530.08860.761-0.20390.8214-64.90629.153-20.826
742.52931.1112-0.58492.95840.76064.7283-0.1701-0.31870.1729-0.17980.1921-0.0612-0.15070.00160.00040.36620.0674-0.11380.3996-0.0090.5267-67.30943-5.196
752.30710.2124-1.11753.94850.97942.9610.0436-0.50760.01590.72060.1527-0.23360.23940.4355-0.00020.51930.1099-0.1670.49-0.02120.6592-69.5439.34410.453
763.01781.6206-0.78253.8833-0.68443.74760.2057-0.60880.55891.2453-0.35550.1944-1.0773-0.1271-0.06320.70680.0266-0.11810.7546-0.16550.907-71.37250.59915.362
773.14661.2127-0.95853.65340.24173.8187-0.2382-0.01270.5283-0.38750.46120.0761-0.2839-0.1199-0.0010.45240.079-0.07520.45990.03710.6366-68.13848.059-10.02
784.28870.32050.58836.10210.43982.3407-0.5920.732-0.8192-0.64640.0982-0.50211.45170.19230.44811.2977-0.10750.0830.9302-0.26651.0179-73.89919.355-19.301
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:139 )A1 - 139
2X-RAY DIFFRACTION2( CHAIN A AND RESID 140:158 )A140 - 158
3X-RAY DIFFRACTION3( CHAIN A AND RESID 159:214 )A159 - 214
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:17 )B2 - 17
5X-RAY DIFFRACTION5( CHAIN B AND RESID 18:90 )B18 - 90
6X-RAY DIFFRACTION6( CHAIN B AND RESID 91:102 )B91 - 102
7X-RAY DIFFRACTION7( CHAIN B AND RESID 103:152 )B103 - 152
8X-RAY DIFFRACTION8( CHAIN B AND RESID 153:210 )B153 - 210
9X-RAY DIFFRACTION9( CHAIN D AND RESID 1:83 )D1 - 83
10X-RAY DIFFRACTION10( CHAIN D AND RESID 84:139 )D84 - 139
11X-RAY DIFFRACTION11( CHAIN D AND RESID 140:158 )D140 - 158
12X-RAY DIFFRACTION12( CHAIN D AND RESID 159:216 )D159 - 216
13X-RAY DIFFRACTION13( CHAIN F AND RESID 2:90 )F2 - 90
14X-RAY DIFFRACTION14( CHAIN F AND RESID 91:102 )F91 - 102
15X-RAY DIFFRACTION15( CHAIN F AND RESID 103:120 )F103 - 120
16X-RAY DIFFRACTION16( CHAIN F AND RESID 121:210 )F121 - 210
17X-RAY DIFFRACTION17( CHAIN H AND RESID 1:99 )H1 - 99
18X-RAY DIFFRACTION18( CHAIN H AND RESID 100:139 )H100 - 139
19X-RAY DIFFRACTION19( CHAIN H AND RESID 140:158 )H140 - 158
20X-RAY DIFFRACTION20( CHAIN H AND RESID 159:216 )H159 - 216
21X-RAY DIFFRACTION21( CHAIN I AND RESID 1:83 )I1 - 83
22X-RAY DIFFRACTION22( CHAIN I AND RESID 84:139 )I84 - 139
23X-RAY DIFFRACTION23( CHAIN I AND RESID 140:158 )I140 - 158
24X-RAY DIFFRACTION24( CHAIN I AND RESID 159:215 )I159 - 215
25X-RAY DIFFRACTION25( CHAIN J AND RESID 1:17 )J1 - 17
26X-RAY DIFFRACTION26( CHAIN J AND RESID 18:90 )J18 - 90
27X-RAY DIFFRACTION27( CHAIN J AND RESID 91:103 )J91 - 103
28X-RAY DIFFRACTION28( CHAIN J AND RESID 104:192 )J104 - 192
29X-RAY DIFFRACTION29( CHAIN J AND RESID 193:210 )J193 - 210
30X-RAY DIFFRACTION30( CHAIN L AND RESID 2:17 )L2 - 17
31X-RAY DIFFRACTION31( CHAIN L AND RESID 18:31 )L18 - 31
32X-RAY DIFFRACTION32( CHAIN L AND RESID 32:47 )L32 - 47
33X-RAY DIFFRACTION33( CHAIN L AND RESID 48:74 )L48 - 74
34X-RAY DIFFRACTION34( CHAIN L AND RESID 75:102 )L75 - 102
35X-RAY DIFFRACTION35( CHAIN L AND RESID 103:131 )L103 - 131
36X-RAY DIFFRACTION36( CHAIN L AND RESID 132:152 )L132 - 152
37X-RAY DIFFRACTION37( CHAIN L AND RESID 153:163 )L153 - 163
38X-RAY DIFFRACTION38( CHAIN L AND RESID 164:182 )L164 - 182
39X-RAY DIFFRACTION39( CHAIN L AND RESID 183:199 )L183 - 199
40X-RAY DIFFRACTION40( CHAIN L AND RESID 200:210 )L200 - 210
41X-RAY DIFFRACTION41( CHAIN C AND RESID 334:349 )C334 - 349
42X-RAY DIFFRACTION42( CHAIN C AND RESID 350:364 )C350 - 364
43X-RAY DIFFRACTION43( CHAIN C AND RESID 365:375 )C365 - 375
44X-RAY DIFFRACTION44( CHAIN C AND RESID 376:393 )C376 - 393
45X-RAY DIFFRACTION45( CHAIN C AND RESID 394:421 )C394 - 421
46X-RAY DIFFRACTION46( CHAIN C AND RESID 422:442 )C422 - 442
47X-RAY DIFFRACTION47( CHAIN C AND RESID 443:459 )C443 - 459
48X-RAY DIFFRACTION48( CHAIN C AND RESID 460:479 )C460 - 479
49X-RAY DIFFRACTION49( CHAIN C AND RESID 480:494 )C480 - 494
50X-RAY DIFFRACTION50( CHAIN C AND RESID 495:516 )C495 - 516
51X-RAY DIFFRACTION51( CHAIN C AND RESID 517:532 )C517 - 532
52X-RAY DIFFRACTION52( CHAIN E AND RESID 334:364 )E334 - 364
53X-RAY DIFFRACTION53( CHAIN E AND RESID 365:375 )E365 - 375
54X-RAY DIFFRACTION54( CHAIN E AND RESID 376:409 )E376 - 409
55X-RAY DIFFRACTION55( CHAIN E AND RESID 410:442 )E410 - 442
56X-RAY DIFFRACTION56( CHAIN E AND RESID 443:474 )E443 - 474
57X-RAY DIFFRACTION57( CHAIN E AND RESID 475:487 )E475 - 487
58X-RAY DIFFRACTION58( CHAIN E AND RESID 488:516 )E488 - 516
59X-RAY DIFFRACTION59( CHAIN E AND RESID 517:531 )E517 - 531
60X-RAY DIFFRACTION60( CHAIN G AND RESID 334:349 )G334 - 349
61X-RAY DIFFRACTION61( CHAIN G AND RESID 350:364 )G350 - 364
62X-RAY DIFFRACTION62( CHAIN G AND RESID 365:375 )G365 - 375
63X-RAY DIFFRACTION63( CHAIN G AND RESID 376:393 )G376 - 393
64X-RAY DIFFRACTION64( CHAIN G AND RESID 394:442 )G394 - 442
65X-RAY DIFFRACTION65( CHAIN G AND RESID 443:459 )G443 - 459
66X-RAY DIFFRACTION66( CHAIN G AND RESID 460:479 )G460 - 479
67X-RAY DIFFRACTION67( CHAIN G AND RESID 480:494 )G480 - 494
68X-RAY DIFFRACTION68( CHAIN G AND RESID 495:516 )G495 - 516
69X-RAY DIFFRACTION69( CHAIN G AND RESID 517:529 )G517 - 529
70X-RAY DIFFRACTION70( CHAIN K AND RESID 333:349 )K333 - 349
71X-RAY DIFFRACTION71( CHAIN K AND RESID 350:364 )K350 - 364
72X-RAY DIFFRACTION72( CHAIN K AND RESID 365:375 )K365 - 375
73X-RAY DIFFRACTION73( CHAIN K AND RESID 376:393 )K376 - 393
74X-RAY DIFFRACTION74( CHAIN K AND RESID 394:459 )K394 - 459
75X-RAY DIFFRACTION75( CHAIN K AND RESID 460:479 )K460 - 479
76X-RAY DIFFRACTION76( CHAIN K AND RESID 480:494 )K480 - 494
77X-RAY DIFFRACTION77( CHAIN K AND RESID 495:516 )K495 - 516
78X-RAY DIFFRACTION78( CHAIN K AND RESID 517:529 )K517 - 529

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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