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- PDB-8df5: SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S... -

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基本情報

登録情報
データベース: PDB / ID: 8df5
タイトルSARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab
要素
  • Angiotensin-converting enzyme 2
  • S304 Fab Heavy Chain
  • S304 Fab Light Chain
  • S309 Fab Heavy Chain
  • S309 Fab Light Chain
  • Spike protein S1
キーワードVIRAL PROTEIN/Hydrolase/Immune System / RBD / SARS-CoV-2 / COVID / S309 / beta / B.1.351 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-Hydrolase-Immune System complex
機能・相同性
機能・相同性情報


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / endopeptidase activity / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Potential therapeutics for SARS / 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 entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / 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 / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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 / Angiotensin-converting enzyme 2
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: 2.7 Å
データ登録者McCallum, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Snell, G. / Veesler, D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: Science / 年: 2022
タイトル: Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution.
著者: Starr, T.N. / Greaney, A.J. / Hannon, W.W. / Loes, A.N. / Hauser, K. / Dillen, J.R. / Ferri, E. / Farrell, A.G. / Dadonaite, B. / McCallum, M. / Matreyek, K.A. / Corti, D. / Veesler, D. / Snell, G. / Bloom, J.D.
履歴
登録2022年6月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年8月3日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: S309 Fab Heavy Chain
B: S309 Fab Light Chain
C: S309 Fab Heavy Chain
D: S309 Fab Light Chain
E: Angiotensin-converting enzyme 2
F: Angiotensin-converting enzyme 2
H: S304 Fab Heavy Chain
L: S304 Fab Light Chain
M: S304 Fab Heavy Chain
N: S304 Fab Light Chain
R: Spike protein S1
S: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)440,01881
ポリマ－433,52112
非ポリマー6,49769
水18,3211017
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: immunoprecipitation
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)78.531, 126.773, 145.663
Angle α, β, γ (deg.)91.780, 103.660, 96.020
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

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タンパク質 , 2種, 4分子 EFRS

#3: タンパク質 Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related ...Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related carboxypeptidase / ACE-related carboxypeptidase / Metalloprotease MPROT15


分子量: 92556.695 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACE2, UNQ868/PRO1885 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: Q9BYF1, angiotensin-converting enzyme 2, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ
#6: タンパク質 Spike protein S1


分子量: 29343.143 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2

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抗体 , 4種, 8分子 ACBDHMLN

#1: 抗体 S309 Fab Heavy Chain


分子量: 24573.471 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#2: 抗体 S309 Fab Light Chain


分子量: 23204.697 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 S304 Fab Heavy Chain


分子量: 23712.402 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 S304 Fab Light Chain


分子量: 23369.947 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 2種, 15分子

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


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#11: 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: 13 / 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, 1071分子

#8: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 30 / 由来タイプ: 合成 / 式: C2H6O2
#9: 化合物...
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 22 / 由来タイプ: 合成 / 式: Cl
#10: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1017 / 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

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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: 3.23 Å3/Da / 溶媒含有率: 61.89 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M Tris (base)/bicine pH 8.5, 3% w/v D- sorbitol

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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: SSRL / ビームライン: BL9-2 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2021年2月19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: 0.9795 Å / 相対比: 1
反射解像度: 2.7→46.27 Å / Num. obs: 180932 / % possible obs: 90.8 % / 冗長度: 3.7 % / Biso Wilson estimate: 57.07 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.057 / Net I/σ(I): 12.3
反射 シェル解像度: 2.7→2.8 Å / Num. unique obs: 13019 / CC1/2: 0.7 / Rpim(I) all: 0.487

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XDS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: 7TN0

7tn0


解像度: 2.7→46.27 Å / SU ML: 0.336 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 22.0388
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2171 7036 5.13 %
Rwork0.1774 130113 -
obs0.1794 137149 92.17 %
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: 65.27 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→46.27 Å
タンパク質核酸リガンド溶媒全体
原子数25506 0 382 1017 26905
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.007126493
X-RAY DIFFRACTIONf_angle_d0.887336054
X-RAY DIFFRACTIONf_chiral_restr0.05093995
X-RAY DIFFRACTIONf_plane_restr0.0074635
X-RAY DIFFRACTIONf_dihedral_angle_d15.05039277
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.28051960.27114233X-RAY DIFFRACTION90.13
2.73-2.760.31992130.28474127X-RAY DIFFRACTION87.78
2.76-2.80.32032170.274034X-RAY DIFFRACTION84.36
2.8-2.830.30062200.27543923X-RAY DIFFRACTION84.07
2.83-2.870.30662450.27144399X-RAY DIFFRACTION94.54
2.87-2.910.32472290.27484518X-RAY DIFFRACTION94.37
2.91-2.950.31052840.26444325X-RAY DIFFRACTION94.18
2.95-2.990.31182650.25154390X-RAY DIFFRACTION94.08
2.99-3.040.28892630.24794435X-RAY DIFFRACTION94.09
3.04-3.090.30532490.2334408X-RAY DIFFRACTION93.83
3.09-3.140.27762340.22174444X-RAY DIFFRACTION93.41
3.14-3.20.25462150.21344354X-RAY DIFFRACTION93.63
3.2-3.260.2622410.20834444X-RAY DIFFRACTION93.63
3.26-3.330.23872680.20634363X-RAY DIFFRACTION93.46
3.33-3.40.24372510.20434374X-RAY DIFFRACTION92.76
3.4-3.480.24142500.19684272X-RAY DIFFRACTION92.02
3.48-3.570.21912470.18564274X-RAY DIFFRACTION90.15
3.57-3.660.23362030.18353921X-RAY DIFFRACTION84.34
3.66-3.770.22362390.17034342X-RAY DIFFRACTION91.36
3.77-3.890.20122340.16214506X-RAY DIFFRACTION95.64
3.89-4.030.18142260.15494490X-RAY DIFFRACTION95.47
4.03-4.190.20392200.14574516X-RAY DIFFRACTION95.41
4.19-4.380.17052230.13544489X-RAY DIFFRACTION94.71
4.38-4.620.15592290.12134439X-RAY DIFFRACTION93.9
4.62-4.90.17842220.13184410X-RAY DIFFRACTION93.05
4.9-5.280.1782420.14294189X-RAY DIFFRACTION89.66
5.28-5.810.18112050.15564231X-RAY DIFFRACTION89.76
5.81-6.650.19232110.17154549X-RAY DIFFRACTION95.93
6.65-8.370.19472550.16294399X-RAY DIFFRACTION94.12
8.37-46.270.17672400.15574315X-RAY DIFFRACTION91.43
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)
14.009548073091.118860231010.02521957457934.50530443895-0.3654620526736.49763118612-0.1555685034920.0327151483930.4590123172210.1165758082810.09604126100950.0225490625528-0.455222079619-0.1449903553530.06397404526970.3072243163280.00192408318769-0.008677023864040.2752258890950.02770620264310.35419433026-18.503629207426.556025516422.1432492872
21.861507217340.276884189243-0.9740001952173.297674468910.52857499323.298177915620.3098649252090.1944232865520.628062271751-0.281071968004-0.116610235281-0.210754985953-0.5494684529630.259948016653-0.007159789510980.434605717294-0.0626576104354-0.04149083153190.4020044762170.08025134744860.486703224145-15.531787347133.549711880322.2396666285
32.250794513390.4543195209720.6325322472822.151875629011.65947791492.505939476810.0917825223366-0.06667423494250.133150713156-0.0968297692108-0.150716853511-0.197778585741-0.0983412242762-0.03262243594590.04675924969980.36071979059-0.05843291055570.02526311205770.2978086333520.07469617937160.306426935134-16.562778178827.059416627837.1512883583
43.78423087035-0.316142396451.492550421994.69134341564-3.202904714746.58380510374-0.117090238113-0.2289199280180.364316894360.173436723253-0.163611015398-0.256267579583-0.3623113230410.5717204052180.2244393687740.366583834272-0.02775823398560.005210962765550.437550334733-0.03150061729630.494277415971-11.107848051232.687199951954.0479701347
54.66847547158-2.403885260245.063052992521.16658745229-2.293786590348.692663667440.04756598846840.1516796335570.0798988702946-0.0557980879986-0.1939586011590.1543189090310.1289589979930.1939481199970.02876871422220.36796145469-0.003144510458790.003327538446410.2960898783520.00921669440260.552147438966-33.602519027910.55283272937.1196762774
61.692934447560.6145190355071.349980682882.03305884611-1.042285660765.946846159890.0885495623460.148087625066-0.0010713510909-0.00438553601395-0.0671143978236-0.2137826975210.04454652352710.404813358853-0.002910688041970.2736030202980.01842830417920.02614270917450.2830297561960.04487110253580.366628541254-25.614980537410.570147699131.6122042813
71.653583300350.5659868677341.927135504055.269776905024.967057793996.86485714926-0.0125871261588-0.207795355931-0.1798926948260.367248667729-0.09714750902250.2740069846140.194923430363-0.576643333267-0.03159992340270.369608094227-0.05036907896680.01277766683710.4191764245440.06784129127970.437594604789-27.434972021413.088744132454.2538423759
82.40494143890.05737430094051.296862911448.373007078573.710278073465.76182847749-0.215017044766-0.3058471364930.4673162740660.03955547991710.2608342855670.1266559413-0.489009577797-0.00157913415053-0.0663407476390.374529276850.03918772765990.0448807219560.417144979247-0.01376858032960.453493263351-21.058213344632.620840631363.7195277229
91.31793521743-0.5374800603150.07876416718298.760320358921.186946029423.204663134280.105445914654-0.4552731850980.2188925513060.605310759681-0.05633775624950.374328304333-0.199417579803-0.100493748352-0.05301335697140.37114362057-0.02341923067380.06270901617380.527029838528-0.01835450442530.458950381093-24.390432280932.243483558565.9331751428
107.07341678043-1.40288374787-1.469357013053.21695529063-1.709566348622.552291022130.5069112912010.331173177155-0.594354186196-0.584455301715-0.05230900956840.3094120460860.470234567153-0.205020553402-0.4857653933120.512703905589-0.0206060164575-0.06792181105580.295509541737-0.007428099598810.511617811938-45.8761116332-40.472445903859.4678265222
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581.81777752193-0.375796502183-0.05460806974154.083335803321.048514053322.28999190238-0.134329519939-0.3471184220260.540524399810.299387666580.006629947323840.17391857221-0.230617464921-0.1011168533610.142673371230.50193425784-0.0446811050150.01897400826130.454688607516-0.06621323260620.542854590505-68.50452281958.157656497429.8860928218
593.035226504292.341282258273.282871817165.003323190472.822688782145.54679731094-0.181132089945-0.2417739470450.06130361312610.1924851262710.02818145301260.666968684006-0.064429075967-0.5913396434280.07409019898220.3188200582570.03532106427440.06237533856070.4462815199940.0586157694230.484818502472-60.6552726862-6.6745798654664.759276573
603.4438117775-0.562827993128-0.2314674477886.861675365641.163026123226.33113846212-0.315093823971-0.146706540748-0.03292003478350.3282589994420.574367818826-0.659199675807-0.358080882620.624025435819-0.1830345487050.3343647860490.0215352438398-0.03687327342190.3912362602810.04412071007910.485679635-48.5800732116-6.7152795914962.7975927277
611.662009331630.976545889966-0.4689426261574.591914163181.479472967345.426745037640.0355952182806-0.119358523745-0.2350395178280.2674277286810.2482254528380.2658986101830.087847849259-0.0538594361374-0.2882350186380.289312457830.03103516121480.005938902040350.3005656135740.08635052081680.444629469763-53.7055380206-10.729190051563.6839025126
621.11241365881-0.128843861821-0.2418057220421.733797296042.394972407393.34071628324-0.406276791522-0.3116866115710.2144610172941.168731491470.220281882612-0.0329049490357-0.452935863455-0.08757446687070.1453193115320.361399852953-0.02356060602750.0692452958060.4538601940810.03193492683280.419278447348-56.684878329218.617287562374.5830526329
631.61329919014-0.7960126192290.8590446364416.79659624809-5.081694465818.99250923263-0.0208825746622-0.01687174190740.2059068661410.06071312122010.2575493188770.518818751723-0.0716940355634-0.625263629307-0.2088725676560.300275424911-0.02058822670570.03288980768080.3854591342180.009016056935190.418203126512-58.025073607220.985041259465.5035362626
645.14873105346-3.4133690651.391604611638.76275091179-2.388762138924.61285127526-0.2390330035140.07540223747920.2181513790261.328810041980.7085029957431.67064327824-0.706658381359-0.621722192353-0.5296153568610.5248409016350.0428845009850.1373885471050.6175031843060.08715080163180.661913209865-66.330833938621.901502123469.1083527096
659.74084139803-8.42178611885.970696201529.59696162964-5.545039152558.658717488680.1853003893340.0681280322397-0.137691948298-0.251689281699-0.15447849043-0.105262668227-0.0159139841320.1289956875580.006232080932970.277788082699-0.01843887794390.03215723937920.296804845746-0.0007977312507730.309679444897-38.04498136552.597063641446.0355228847
661.444989940060.09821257278-0.2690037942595.1085282563-0.8604240469442.004433442040.04788494323740.0233030942035-0.0785595064416-0.0111459859951-0.009246572254080.2795333636460.0305529287421-0.0637790891612-0.06008669992710.324752248536-0.02988694872-0.006737101283720.334108798570.02131319419250.318868968669-46.0235806944-3.226781211146.8023838495
670.452219216153-1.505346784350.1774609067986.74105912613-0.3712436069720.2937791881690.157912577191-0.000733539001999-0.0157187924701-0.285839432749-0.331733930286-0.447667590011-0.21540999408-0.224301898430.1918323251660.4349084381930.03141656667910.06624402941140.3371025098650.0247966740340.359199360492-44.296002552519.549346161547.0731513398
684.03725857956-0.2335716858261.28967035728.74081863321-0.9930913213612.042828843660.065952826299-0.5563050496810.376636101710.9968332797230.2025765225091.04963142680.0511871669864-1.21695874077-0.4203022365440.4334804292920.009065479024970.09915889267260.476448901762-0.01167093066860.548250260253-57.088714032632.437769107371.5419482028
693.27801164517-1.53993923876-2.408222938746.005966851795.713747639625.84103757123-0.3024820505320.00791458921613-0.06703990852640.1349656418180.0960377221966-0.06487363836130.01868043307810.2584822667440.2893143709640.4061641409590.0764416670671-0.01165633412820.4211666254110.08092971698790.443372234228-46.65166373729.584636876761.4948946045
701.917725098554.072892406012.472921567992.051279639558.156708326867.128008299420.0878932522244-0.05931899845610.386427338846-0.504809677005-0.0787945351767-0.715668221337-0.1268024223260.152978770732-0.1024878051920.50321600268-0.00524469714763-0.0941007594830.428601334320.08313083995080.818952693852-42.719889861531.814883625869.9765824729
711.916656506981.0832916377-0.48572521988.287072977764.146050554389.27638914480.00896134648759-0.08591839748440.104597054299-0.00135650259765-0.06635129223450.8882394982830.243668507439-0.5674021052330.124725611180.4468076494930.107613435623-0.01972786128140.3884012742950.01313626163320.469887105043-50.49085469319.026361401751.3211883293
721.22581616637-0.1147363746140.3544386244775.380863936283.866704607496.582608701580.122996506716-0.01834379585860.397356773356-0.211871076976-0.06977677565920.436520553249-0.966677611425-0.006226226334670.12014067620.4525739457190.01985370251920.01905630014760.3545514492460.01365215882180.485733493115-48.593744738437.526098715967.7304762622
736.69486349536-4.21429598161-2.151299233182.09571842723.579017643923.5255071985-0.358011686986-0.4135381302830.8075173963171.178271979950.199145893408-0.894922264921-0.5395967410680.6558131547150.1005199891670.577333973503-0.192291746188-0.08372721341350.4522530148040.0664008798440.619144909187-13.839551316233.207719784630.8051680216
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 'M' and (resid 18 through 66 )MW18 - 6618 - 66
22chain 'M' and (resid 67 through 90 )MW67 - 9067 - 90
33chain 'M' and (resid 91 through 141 )MW91 - 14191 - 138
44chain 'M' and (resid 142 through 221 )MW142 - 221139 - 218
55chain 'N' and (resid 1 through 25 )NX1 - 251 - 25
66chain 'N' and (resid 26 through 102 )NX26 - 10226 - 102
77chain 'N' and (resid 103 through 114 )NX103 - 114103 - 114
88chain 'N' and (resid 115 through 151 )NX115 - 151115 - 151
99chain 'N' and (resid 152 through 215 )NX152 - 215152 - 215
1010chain 'R' and (resid 330 through 349 )RY330 - 3491 - 20
1111chain 'R' and (resid 350 through 367 )RY350 - 36721 - 38
1212chain 'R' and (resid 368 through 409 )RY368 - 40939 - 80
1313chain 'R' and (resid 410 through 459 )RY410 - 45981 - 130
1414chain 'R' and (resid 460 through 494 )RY460 - 494131 - 165
1515chain 'R' and (resid 495 through 529 )RY495 - 529166 - 200
1616chain 'S' and (resid 332 through 358 )SAC332 - 3581 - 27
1717chain 'S' and (resid 359 through 393 )SAC359 - 39328 - 62
1818chain 'S' and (resid 394 through 516 )SAC394 - 51663 - 185
1919chain 'S' and (resid 517 through 529 )SAC517 - 529186 - 198
2020chain 'A' and (resid 1 through 125 )AA1 - 1251 - 125
2121chain 'A' and (resid 126 through 148 )AA126 - 148126 - 144
2222chain 'A' and (resid 149 through 228 )AA149 - 228145 - 224
2323chain 'B' and (resid 1 through 18 )BB1 - 181 - 18
2424chain 'B' and (resid 19 through 30 )BB19 - 3019 - 30
2525chain 'B' and (resid 31 through 49 )BB31 - 4931 - 49
2626chain 'B' and (resid 50 through 76 )BB50 - 7650 - 76
2727chain 'B' and (resid 77 through 91 )BB77 - 9177 - 91
2828chain 'B' and (resid 92 through 113 )BB92 - 11392 - 113
2929chain 'B' and (resid 114 through 150 )BB114 - 150114 - 150
3030chain 'B' and (resid 151 through 163 )BB151 - 163151 - 163
3131chain 'B' and (resid 164 through 174 )BB164 - 174164 - 174
3232chain 'B' and (resid 175 through 188 )BB175 - 188175 - 188
3333chain 'B' and (resid 189 through 214 )BB189 - 214189 - 214
3434chain 'C' and (resid 1 through 73 )CC1 - 731 - 73
3535chain 'C' and (resid 74 through 138 )CC74 - 13874 - 138
3636chain 'C' and (resid 139 through 189 )CC139 - 189139 - 189
3737chain 'C' and (resid 190 through 230 )CC190 - 230190 - 230
3838chain 'D' and (resid 1 through 18 )DD1 - 181 - 18
3939chain 'D' and (resid 19 through 30 )DD19 - 3019 - 30
4040chain 'D' and (resid 31 through 49 )DD31 - 4931 - 49
4141chain 'D' and (resid 50 through 62 )DD50 - 6250 - 62
4242chain 'D' and (resid 63 through 76 )DD63 - 7663 - 76
4343chain 'D' and (resid 77 through 91 )DD77 - 9177 - 91
4444chain 'D' and (resid 92 through 113 )DD92 - 11392 - 113
4545chain 'D' and (resid 114 through 150 )DD114 - 150114 - 150
4646chain 'D' and (resid 151 through 163 )DD151 - 163151 - 163
4747chain 'D' and (resid 164 through 174 )DD164 - 174164 - 174
4848chain 'D' and (resid 175 through 214 )DD175 - 214175 - 214
4949chain 'E' and (resid 19 through 51 )EE19 - 511 - 33
5050chain 'E' and (resid 52 through 109 )EE52 - 10934 - 91
5151chain 'E' and (resid 110 through 157 )EE110 - 15792 - 132
5252chain 'E' and (resid 158 through 346 )EE158 - 346133 - 321
5353chain 'E' and (resid 347 through 431 )EE347 - 431322 - 406
5454chain 'E' and (resid 432 through 612 )EE432 - 612407 - 587
5555chain 'F' and (resid 19 through 109 )FM19 - 1091 - 91
5656chain 'F' and (resid 110 through 157 )FM110 - 15792 - 135
5757chain 'F' and (resid 158 through 431 )FM158 - 431136 - 409
5858chain 'F' and (resid 432 through 614 )FM432 - 614410 - 592
5959chain 'H' and (resid 1 through 33 )HU1 - 331 - 33
6060chain 'H' and (resid 34 through 51 )HU34 - 5134 - 51
6161chain 'H' and (resid 52 through 116 )HU52 - 11652 - 116
6262chain 'H' and (resid 117 through 141 )HU117 - 141117 - 135
6363chain 'H' and (resid 142 through 197 )HU142 - 197136 - 191
6464chain 'H' and (resid 198 through 223 )HU198 - 223192 - 217
6565chain 'L' and (resid 1 through 25 )LV1 - 251 - 25
6666chain 'L' and (resid 26 through 102 )LV26 - 10226 - 102
6767chain 'L' and (resid 103 through 114 )LV103 - 114103 - 114
6868chain 'L' and (resid 115 through 129 )LV115 - 129115 - 129
6969chain 'L' and (resid 130 through 151 )LV130 - 151130 - 151
7070chain 'L' and (resid 152 through 164 )LV152 - 164152 - 164
7171chain 'L' and (resid 165 through 175 )LV165 - 175165 - 175
7272chain 'L' and (resid 176 through 215 )LV176 - 215176 - 215
7373chain 'M' and (resid 1 through 17 )MW1 - 171 - 17

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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://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る