[日本語] English
万見
- PDB-7xa7: Crystal structure of SARS-CoV-2 receptor-binding domain in comple... -

+
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: 7xa7
タイトルCrystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2
要素
  • Angiotensin-converting enzyme
  • Spike protein S1
キーワードVIRAL PROTEIN / complex
機能・相同性
機能・相同性情報


加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space ...加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / 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 / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / 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 / proteolysis / extracellular space / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
類似検索 - 分子機能
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
類似検索 - ドメイン・相同性
Angiotensin-converting enzyme / Spike glycoprotein
類似検索 - 構成要素
生物種Rhinolophus affinis (ナカキクガシラコウモリ)
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: 3.31 Å
データ登録者Tang, L.F. / Zhang, D. / Han, P. / Qi, J.X.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)32192452 中国
引用ジャーナル: Int J Biol Sci / 年: 2022
タイトル: Structural basis of SARS-CoV-2 and its variants binding to intermediate horseshoe bat ACE2.
著者: Tang, L. / Zhang, D. / Han, P. / Kang, X. / Zheng, A. / Xu, Z. / Zhao, X. / Wang, V.Y. / Qi, J. / Wang, Q. / Liu, K. / Gao, G.F.
履歴
登録2022年3月17日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年12月21日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
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: Angiotensin-converting enzyme
B: Spike protein S1
C: Angiotensin-converting enzyme
D: Spike protein S1
E: Angiotensin-converting enzyme
F: Spike protein S1
G: Angiotensin-converting enzyme
H: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)380,49416
ポリマ－379,3478
非ポリマー1,1468
水75742
1
G: Angiotensin-converting enzyme
H: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,1234
ポリマ－94,8372
非ポリマー2872
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Angiotensin-converting enzyme
B: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,1234
ポリマ－94,8372
非ポリマー2872
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-38 kcal/mol
Surface area34610 Å2
手法PISA
3
C: Angiotensin-converting enzyme
D: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,1234
ポリマ－94,8372
非ポリマー2872
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-34 kcal/mol
Surface area34350 Å2
手法PISA
4
E: Angiotensin-converting enzyme
F: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,1234
ポリマ－94,8372
非ポリマー2872
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-37 kcal/mol
Surface area34150 Å2
手法PISA
単位格子
Length a, b, c (Å)63.943, 130.849, 564.829
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

-
要素

#1: タンパク質
Angiotensin-converting enzyme


分子量: 69714.430 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Rhinolophus affinis (ナカキクガシラコウモリ)
発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A7D7FA76, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素
#2: タンパク質
Spike protein S1


分子量: 25122.336 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 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#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: 4 / 由来タイプ: 合成 / 式: C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 42 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

-
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: 3.23 Å3/Da / 溶媒含有率: 61.95 %
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: 0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5, 5 % (w/v) PEG 4000

-
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: NFPSS / ビームライン: BL19U1 / 波長: 0.979 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: 0.979 Å / 相対比: 1
反射解像度: 3.3→50 Å / Num. obs: 69914 / % possible obs: 96.5 % / 冗長度: 8.9 % / Biso Wilson estimate: 86.59 Å2 / Rmerge(I) obs: 0.218 / Net I/σ(I): 8.8
反射 シェル解像度: 3.3→3.42 Å / 冗長度: 8.3 % / Rmerge(I) obs: 1.345 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7015 / % possible all: 99.2

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.19rc3_4028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
開始モデル: 6LZG

6lzg


解像度: 3.31→40.28 Å / SU ML: 0.4338 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.1561
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2537 1993 2.86 %
Rwork0.2328 67665 -
obs0.2333 69658 96.08 %
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: 90.55 Å2
精密化ステップサイクル: LAST / 解像度: 3.31→40.28 Å
タンパク質核酸リガンド溶媒全体
原子数25740 0 60 42 25842
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001926536
X-RAY DIFFRACTIONf_angle_d0.487136032
X-RAY DIFFRACTIONf_chiral_restr0.03823740
X-RAY DIFFRACTIONf_plane_restr0.00464660
X-RAY DIFFRACTIONf_dihedral_angle_d4.0733500
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.390.36061400.35394740X-RAY DIFFRACTION95.05
3.39-3.480.37291430.31594855X-RAY DIFFRACTION99.62
3.48-3.580.31991470.29814982X-RAY DIFFRACTION99.77
3.58-3.70.30121440.28454893X-RAY DIFFRACTION99.62
3.7-3.830.3281470.27314971X-RAY DIFFRACTION99.44
3.83-3.990.29971460.25434952X-RAY DIFFRACTION99.18
3.99-4.170.23821440.25184886X-RAY DIFFRACTION98.69
4.17-4.390.24281430.23044882X-RAY DIFFRACTION97.86
4.39-4.660.22411450.21624891X-RAY DIFFRACTION97.45
4.66-5.020.21431430.20964859X-RAY DIFFRACTION96.68
5.02-5.520.27791430.21814835X-RAY DIFFRACTION96.16
5.52-6.320.27311430.23424870X-RAY DIFFRACTION95.14
6.32-7.950.20531400.20694751X-RAY DIFFRACTION92.32
7.95-40.280.18041250.16954298X-RAY DIFFRACTION79.75
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)
11.70812411760.06024381403391.208499608880.161698057814-0.1543147014580.31470815964-0.05014468951520.298971832280.0623000447496-0.2415381642020.0528948699439-0.160246747456-0.2388871888180.2589727914820.006933906577530.8490032618840.007326582316880.1807457505140.941893157578-0.06912551882080.59130016862619.614176374220.657101940634.5641859578
21.060491479860.2066102782950.2517717112632.022211195150.0122390226232.076569529460.06779818357650.1120878864-0.0977356647399-0.5691473591570.0510508683688-0.42383317952-0.03444414201480.0898031523829-0.1094570289360.5217734290570.05313082439320.154974255190.711864639201-0.08815838914420.44243478432224.82092289417.2405708062150.6817068475
30.904270535945-0.3385889285550.7428182714611.960874784240.8758263761492.692391992560.0969418787994-0.118845628926-0.0271416211211-0.04196739250280.0474595308853-0.169578835523-0.140728934259-0.423817688378-0.1498637073280.5021140155420.01873605143620.07362221188640.657745435219-0.03739954817910.38655036560423.846089079411.980944805459.6906081404
45.63275373314-0.4933584015651.051183243110.240872803355-1.200701242685.56652782247-0.1620558654791.51645499166-0.6927894784-0.264793840551-0.2708988411950.3100829905080.491840506456-0.1717541182420.5844885420520.962231570121-0.02310935393170.04720266138291.16615614599-0.2123725922340.562720227162-17.0919835411-0.51653533927210.5719989758
52.073100784073.408161101251.510881179592.1379601258-1.648806278084.418051929840.3831849844160.387267816717-1.516404087220.321396855166-0.5086275429390.1044773338691.05082687504-1.46580950301-0.182343306241.26988773071-0.139422225657-0.03297144727231.14777549818-0.403392478140.938898295607-21.6326182265-9.3886707726121.2391315618
62.023954959173.163743775691.151582791152.20063510445-1.805983372574.11787149249-0.0735849544504-0.1385742811420.06954364512680.848563334202-0.851247375267-0.1080694516970.246213048044-0.5396608319960.3609325123060.999685434828-0.03725263118330.08058560104091.27239823196-0.4850104472920.314532748764-13.64190942764.3832042353821.9166876103
76.085047337562.000077113483.396491754684.28079055481-0.7073947465662.790889257980.4566586048960.19985425888-0.303024501592-0.016651431887-0.5521294747180.78637599882-0.236813643996-0.3785740223320.1068247181480.8063830086080.04992748307410.03520242181890.922478844639-0.2792230932790.462772028578-14.70102191685.0036973007324.3676756436
80.2638076299820.5322896157820.7371513974640.6693800598770.1896568111591.612021603940.2079043534650.146319963230.0629097480913-0.114906616375-0.1813081709680.0884684178135-0.1272598302550.1239481128010.03114434747480.7942355936840.04585195202310.0753166504661.08523337732-0.08411040346150.434202788065-7.9547797946716.077740067821.2268953187
99.214558309197.101109234265.960124442769.934145457874.654104604753.8627498996-0.6428027541911.3580173851-0.801972641576-1.76792309487-0.1043584386180.845934311073-1.203046872020.9975948719650.7411504657261.30831233875-0.1486388408460.2944690746561.17238452358-0.39432421940.86970570196-33.6108864601-5.5803908625111.691375979
100.3170042067930.512633663814-0.02328660132321.45835261637-1.291232321351.03902300657-0.206908098194-0.397123129382-0.200466916987-0.161503079403-0.105017653303-0.7201501431620.34480028480.6354200422630.3520653306110.6505721615960.2226181195750.05991924277221.367455809330.01054627460020.892805564562.0906978390569.9835896787106.87818423
112.67718424973-0.05235082385430.9623638460542.33282435291-0.7127245379671.69319085626-0.223015097997-0.139370803670.0237125983949-0.3974018677260.0078932852887-0.02544681943880.154291518787-0.1090288393040.1983206430570.6308473643080.04921497855150.08710215237280.752901329501-0.08819210975620.347638487122-7.0488349255487.299056424985.826291693
121.869343290010.909931128837-0.7932242683513.72823870709-1.880292511871.31789560823-0.1549397245430.0645033125398-0.0820142763813-0.3490257673610.2192110474680.333607619813-0.0764829362313-0.329531602096-0.1204731821810.560785510030.0562155196728-0.07566763730870.720579878265-0.1464211228320.407758747056-27.982181584680.628107719590.0723039378
136.94228629687-0.4493717330632.427237804413.63417124001-0.6347572078443.865062155620.00602863949845-0.7476067617170.7279462528740.0655041600247-0.0660719725087-0.125131460818-0.08935804415960.1011079438610.1459298893740.3594249352590.05752380700840.06519418335450.921274713266-0.09144181698560.465628302994-21.758856328673.4292405805103.983768078
141.027197999740.801581598393-0.2888671621822.62852600791-0.1101327984691.00930266522-0.1624696287410.107531681546-0.0296101500038-0.6889357087970.0085824528830.02937396996310.0656573004266-0.02078680331260.1534845430450.6201721423040.04871704023290.01568317898510.891070023106-0.1257871725230.359953580827-13.377123270281.455469564684.4962993213
151.575146060.61955450558-0.650799038263.33899066081-1.182392569422.52667027931-0.2862073363750.445132126631-0.251606696582-1.011857462140.1109290591970.01925614689560.5619541323640.09684284458420.1761891251780.792633639848-0.01981601486870.03196934699350.693669619317-0.157438907190.438279288939-18.575333222770.069220514378.9467979256
160.2874681020631.376515059990.7658860476667.955432218471.463277581834.44511472462-0.155959314170.0736469419205-0.248487657360.518957976685-0.4166975950961.647928481220.299906382403-1.122318853180.499362264990.5915476695810.1303125601510.2190173514791.446530876860.1615238391291.22722161543-22.48551567938.0706027157128.584168054
172.76059330830.314931684615-0.437516681643.84369230742-0.4024759408282.39880416762-0.22078422318-0.418737248324-0.429407981249-0.1559677392480.0988881099448-0.8074646158570.5693069989381.052138898270.144063158230.6478351885270.2339465864820.06511763651.154836050590.1630971644110.663709355821-5.7768634156247.7191576236119.938548132
182.99399910630.369427557656-0.3688797990363.93064775063-0.4845629141682.700500307150.0304933948736-0.419622961586-1.317604978590.453375659181-0.09814544808760.07982120965441.083997371610.1822228570540.144769094720.8607613106240.191007138608-0.02347385201231.065005562310.1867969511310.959885724044-20.169484698832.3262316351128.987048027
193.10257136342-0.25232551111-1.008155585462.56166270282-0.3453021882273.1438968010.02572723620380.8523696763610.1119399310280.0860198397655-0.0133886439498-0.3671053312480.1996446944140.2688101144620.02902089548010.400761530140.100381223175-0.06044737726450.976776332805-0.1860999388230.80198273387529.3952449329-9.4284650428198.1039089855
201.946165268153.00876736925-1.323286646524.91322573424-1.643977855831.20240174995-0.1357902413390.117709602891-1.03723214264-0.141238373442-0.215165119502-1.191513126330.214393844746-0.2367658160320.3837158496760.5461610013180.112201191554-0.03633341795171.2265862112-0.2130699976030.98231675459931.4000449825-19.64363019108.609064506
210.3779455685430.00753993202779-0.679895231943.303214773581.503862917813.36910684382-0.231973710110.983561773537-0.0885009424071-0.392706867347-0.3640734957130.910239750110.0515026326403-1.429175738940.6967792035470.654870879596-0.0235817564429-0.006160892205861.36367135688-0.3440786797481.013437766114.40744292077-29.1468586334118.041954944
220.975569950011-0.240690852843-0.9305143251474.0376389461.887224302914.528547239720.279664310662-0.07193168568990.04636544604980.0141068703086-0.270282992539-0.15096863218-0.1998227460940.3168818856110.006173602335140.4142288445690.00313670627129-0.1307766118130.832268545201-0.06411594268710.3911108046522.3037901325-15.7009801664130.301317078
231.192616044760.102514961043-0.3989141750931.57530714868-1.351785525241.929970494650.1706319957830.09474003368070.107401055620.0389742628399-0.02644518578220.606734708963-0.0453293223599-0.708374250029-0.1434793476440.4761438988160.0450793344228-0.0009115155640791.1990156645-0.326723345640.7723705876769.0065605639-7.93719608902121.044254562
242.604206045982.13998177282-1.639581270262.68371245401-2.340169256333.040845397990.2856066470640.0498296652702-0.1263038909880.440775391093-0.200948586633-0.146706271487-0.307770494898-0.113180959055-0.08820646708040.460169108765-0.016055025254-0.03875243316731.05863127272-0.1906339693620.66962417161916.8763479517-2.5361506758132.436261678
255.117351591360.971181027787-1.825223898876.42825528024-0.09610160999974.82975947196-0.4888676890320.845826012992-0.628356574989-0.3082319137430.2304834541790.395432270027-0.687309212786-0.7799833537990.2476247047720.5185616139850.0490162670848-0.01889481323721.15098567159-0.1600456077330.70530097177131.613844451819.83896438379.0461744035
267.74401115026-1.67542622465-0.8170418812697.90659183142-1.686891015776.19382170409-0.319279325561-0.2187496205241.358743681260.1239657526610.2085321300570.529549392116-1.45038588869-0.5286939989680.02826336892480.8029412190250.149415497494-0.1249516802170.831918062354-0.1546691948421.1075736760332.101438884931.618743725185.3940749805
274.108136982471.33074117662-0.8406950309469.57638210403-1.350027933316.70476772430.089733452916-0.0113470081464-0.03311965997660.5027367689360.110055664849-0.576152181441-0.6849621385651.01219663212-0.2401006960180.414901098369-0.06350940046470.02869126094790.728016638038-0.1680737067780.5834756608536.579921324517.849875645391.738999711
281.691691994041.07845576476-0.9511359701843.136194199180.8905602679724.692141896040.0666675563515-0.450521257362-0.1016958924220.00792533626771-0.0992406597732-1.97678091447-0.6753383574091.315537692340.1346113471690.433926364375-0.0429360368194-0.1879558841031.27142860188-0.2147173460491.1526553714243.252910696518.246345595592.9245385824
292.173904981544.17693725917-0.4828929487467.79736027925-0.9784896965824.09882936091-0.156970563709-0.062313875910.352526734638-0.350234824640.3914267534610.137571163882-0.104367437183-0.228261128905-0.06680572293180.4254957638130.2280295835050.02264168901270.789826353665-0.1053541360840.4201559542131.63590059719.0461411404788.3547677968
300.1429999814740.947378775483-0.09500509441256.06480491999-2.043519948964.40362632549-0.309046386555-0.0959589481994-1.04598764013-0.385609394412-0.39707119649-1.814714029660.338808610180.9044411556540.4187273779860.29466400198-0.07408303357820.07959427413381.15634404003-0.03969208408111.2375079044449.62996518665.589279804488.4430212744
310.53544609833-0.7658648078720.5674267588918.10108854295-2.876275036134.44311813133-0.171570143131-0.275528354694-0.411411257867-0.95378563397-0.543419975868-1.653314562760.9543074341710.7792401351870.3417266462770.590756344360.1695306680940.1413167739981.15151141921-0.1910505794680.91206495635545.9861958873-5.6242405730789.7538383634
320.981294175332-0.8800044183310.2220079824078.04688871187-2.645429195784.43933756509-0.195769142063-0.664746686265-0.223122318944-0.07152876834730.5185311496240.418256163805-0.501345774918-0.703159548729-0.3779808125230.3569410090460.157903994526-0.03448322996940.989009230882-0.1273494889850.62282304349228.881605103113.47950866790.3604192286
335.61589542954-6.14917423951-0.07398937670199.90410392894-2.432633302825.536215189060.3761878879330.6302496463560.382899175181.06821500187-1.240517339420.668387998569-0.7797398327890.8079102306760.8326837089541.168094823560.1112881579550.05892384218170.9316938847970.1480451402131.2223607115741.301933954438.811946669778.7648591573
342.0678579782-1.43292243232.783271928666.83203157011-3.176406604064.21821495485-0.500956351699-0.02797718967990.3869564025573.884787044980.320536360468-0.849189420586-1.39209126271-0.2472767951420.3489096253281.59876552423-0.129759349956-0.04965465313071.12478967276-0.2179939422680.7244652068430.479936808680.477033458240.2976513641
351.626367905831.17871411226-0.428115801330.8603912027220.2443068442471.11868467255-0.070004010266-0.2157738272470.1332433464470.175633652804-0.3265364304410.1856173659510.272880408046-0.3330024864150.4437474942171.0653514388-0.000364696161910.04700439674750.884235802695-0.1201678106570.62049097406918.501212569778.21586611134.863768014
361.926556321840.5106727964390.2793772301614.126479033821.607423700140.977725249765-0.0677326801335-0.496530959225-0.08130844479731.48822700231-0.1144336481190.2403013614470.448496972727-0.5608158526730.3742908369721.20262878829-0.09033254286320.2408904150991.04052804146-0.09704520976510.5731448290018.4597114064454.997225175221.5405335123
371.831594943510.6886781478730.3731132289474.391823245981.565404064220.701995610518-0.3592385457950.177355612170.255123327846-0.2041246012130.1866828161660.193801615611-0.406026863498-0.1110317291690.08577796250611.201512165040.0762699283761-0.02150957599440.861775516191-0.01174614128950.40654350045422.847185566170.70648798468.53629032912
382.31000595884-0.6578875921850.8498537721231.967455440740.7436428518522.914010242010.0346455167630.10294586764-0.2748015435460.566396144198-0.2229986687410.04581522379120.6297431451020.07432664906480.1677002508311.05989146488-0.1385619706080.06132246242730.82677793171-0.0451089174220.5082213099831.783161881448.18429221115.3052406945
392.70235594246-0.62593317148-0.1465871971892.62344017510.6582635882643.09357463413-0.0896831956184-0.953153905574-0.04375262186641.04181040399-0.4900815669590.220339173583-0.5347032505210.5991264012510.6060891760881.4591288025-0.0742653548325-0.06553972482061.12746270670.01494691474650.52827017339437.933869291760.102967634533.2251469827
402.14371102316-0.4241195632910.3467894633172.396287723490.1939625083682.110022327080.02444476181-0.1901152502990.05762348266980.460913895255-0.00227206475229-0.459827000311-0.146645516090.280191188458-0.02793394026711.24973398699-0.0859923773203-0.2405163442751.10047082-0.05968390469550.45105128302341.481353287160.18352030219.1114056999
410.977960980242-0.29795567185-0.9022933681671.896544330920.841384066891.557583180040.1494056044040.08470612929420.2251674304990.0298563442652-0.2867289540930.214343810842-0.249272661836-0.4510026917810.1519079458881.135731203120.0441286024268-0.002101932673271.09776743178-0.1809241428750.48926560377315.086687868962.079102869810.9875850044
423.053963448590.05130551674551.081744967811.94721635783-0.2889849967521.54209055495-0.0870844651795-0.2197040266070.1126857887420.644393931901-0.265695832346-0.206808786885-0.4063930678270.1489845356710.1665119964170.992723216589-0.269022789569-0.07470296123690.885934295113-0.04892844017580.51451487170141.618024053169.728374746814.0724792476
432.971565424440.3579752895590.9027476052361.64900344569-0.4183478576921.404658098220.1750363906780.489762388741-0.4340760251740.2366268205640.0150286626769-0.0699460335627-0.106734070126-0.185464362588-0.1156346555870.920201795356-0.0211328640865-0.08840384598850.98672132764-0.08709049615210.40493869919626.943665370258.3876807908-1.02704322178
440.943211920742-0.854388637677-1.534786085242.807695133161.521325041372.57949355679-0.2341062013310.577147431698-0.0422561766974-0.1969908611770.49101439075-0.380224747066-0.7506011892720.656905614153-0.205519680981.40333151656-0.191039502669-0.04897176286611.34252843174-0.1952083302370.66720593810656.651536002985.012326498460.1696030038
451.885343483782.05988942498-1.807844994643.73934088875-0.8741709063034.94968868526-0.1657210044-0.0752772757557-0.579906965234-1.18553319940.282706894436-1.887046184960.1448714771461.21402789887-0.1988775281581.14127271842-0.07294753810980.29662273141.50743165073-0.0725216238711.1841621677468.716382870283.162352748951.391640086
461.803601798940.4864458323380.4937942396992.33194308561.121608067062.94958093356-0.409473723050.7690914541510.213619422496-1.442938844760.381218772897-0.1539107171190.1080531493540.3561247756810.05414498932071.70966720602-0.3150324661540.02829995427221.29648967885-0.03398074422810.56753901651548.929205598287.885997345648.8697925507
474.0956121151-5.949915888542.427974380678.7718010508-3.839311654091.897425692720.506950100774-0.00766741347417-0.66448427503-0.8313671245810.2681637308051.30110582364-0.555611791978-0.125923861831-0.7126473700111.18280114185-0.0724806733046-0.1860051342270.9116115743540.07202395166691.0212428759328.640165172697.05539132849.325580722
482.30599293549-0.4334869440780.6892121753423.05707359623-0.6717130010070.3124704667810.676373415303-0.289714876907-0.13943917348-1.32378187541-0.00928353089637-0.2766824238210.148276156252-0.105373631245-0.1399631317081.99692596802-0.3854260900120.118394095161.24158998851-0.1901889343810.35564618799949.230430933679.305462324349.0447654064
492.19536720973-0.5057717547140.7364841522153.12217271408-0.4081894495570.24881994268-0.047955356569-0.2175147174850.535347950389-0.632968161112-0.566241219122-1.676170843550.1503467645210.04903487029350.3574561055781.56666731588-0.5758103195720.2508690719391.71204079790.1544684145371.7993267509374.018398462594.751319465758.626547266
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 'A' and (resid 2 through 140 )AA2 - 1401 - 139
22chain 'A' and (resid 141 through 448 )AA141 - 448140 - 447
33chain 'A' and (resid 449 through 597 )AA449 - 597448 - 596
44chain 'B' and (resid 334 through 364 )BB334 - 3641 - 31
55chain 'B' and (resid 365 through 393 )BB365 - 39332 - 60
66chain 'B' and (resid 394 through 409 )BB394 - 40961 - 76
77chain 'B' and (resid 410 through 442 )BB410 - 44277 - 109
88chain 'B' and (resid 443 through 516 )BB443 - 516110 - 183
99chain 'B' and (resid 517 through 528 )BB517 - 528184 - 195
1010chain 'C' and (resid 2 through 112 )CD2 - 1121 - 111
1111chain 'C' and (resid 113 through 234 )CD113 - 234112 - 233
1212chain 'C' and (resid 235 through 313 )CD235 - 313234 - 312
1313chain 'C' and (resid 314 through 370 )CD314 - 370313 - 369
1414chain 'C' and (resid 371 through 495 )CD371 - 495370 - 494
1515chain 'C' and (resid 496 through 597 )CD496 - 597495 - 596
1616chain 'D' and (resid 334 through 393 )DE334 - 3931 - 60
1717chain 'D' and (resid 394 through 506 )DE394 - 50661 - 173
1818chain 'D' and (resid 507 through 528 )DE507 - 528174 - 195
1919chain 'E' and (resid 2 through 65 )EG2 - 651 - 64
2020chain 'E' and (resid 66 through 112 )EG66 - 11265 - 111
2121chain 'E' and (resid 113 through 176 )EG113 - 176112 - 175
2222chain 'E' and (resid 177 through 234 )EG177 - 234176 - 233
2323chain 'E' and (resid 235 through 495 )EG235 - 495234 - 494
2424chain 'E' and (resid 496 through 597 )EG496 - 597495 - 596
2525chain 'F' and (resid 334 through 353 )FH334 - 3531 - 20
2626chain 'F' and (resid 354 through 393 )FH354 - 39321 - 60
2727chain 'F' and (resid 394 through 416 )FH394 - 41661 - 83
2828chain 'F' and (resid 417 through 430 )FH417 - 43084 - 97
2929chain 'F' and (resid 431 through 459 )FH431 - 45998 - 126
3030chain 'F' and (resid 460 through 479 )FH460 - 479127 - 146
3131chain 'F' and (resid 480 through 494 )FH480 - 494147 - 161
3232chain 'F' and (resid 495 through 516 )FH495 - 516162 - 183
3333chain 'F' and (resid 517 through 528 )FH517 - 528184 - 195
3434chain 'G' and (resid 2 through 35 )GJ2 - 351 - 34
3535chain 'G' and (resid 36 through 112 )GJ36 - 11235 - 111
3636chain 'G' and (resid 113 through 177 )GJ113 - 177112 - 176
3737chain 'G' and (resid 178 through 234 )GJ178 - 234177 - 233
3838chain 'G' and (resid 235 through 300 )GJ235 - 300234 - 299
3939chain 'G' and (resid 301 through 370 )GJ301 - 370300 - 369
4040chain 'G' and (resid 371 through 414 )GJ371 - 414370 - 413
4141chain 'G' and (resid 415 through 495 )GJ415 - 495414 - 494
4242chain 'G' and (resid 496 through 557 )GJ496 - 557495 - 556
4343chain 'G' and (resid 558 through 597 )GJ558 - 597557 - 596
4444chain 'H' and (resid 334 through 358 )HK334 - 3581 - 25
4545chain 'H' and (resid 359 through 393 )HK359 - 39326 - 60
4646chain 'H' and (resid 394 through 469 )HK394 - 46961 - 136
4747chain 'H' and (resid 470 through 494 )HK470 - 494137 - 161
4848chain 'H' and (resid 495 through 516 )HK495 - 516162 - 183
4949chain 'H' and (resid 517 through 528 )HK517 - 528184 - 195

+
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://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