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- PDB-6sne: crystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide -

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基本情報

登録情報
データベース: PDB / ID: 6sne
タイトルcrystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide
要素
  • Envelope glycoprotein gp160
  • LN01 heavy chain
  • LN01 light chain
キーワードIMMUNE SYSTEM (免疫系) / gp41 / antibody (抗体) / complex / MPER
機能・相同性
機能・相同性情報


virus-mediated perturbation of host defense response => GO:0019049 / : / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity ...virus-mediated perturbation of host defense response => GO:0019049 / : / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 生体膜 / 細胞膜
類似検索 - 分子機能
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Gp120 (HIV) / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 抗体 / Immunoglobulin-like / サンドイッチ / Mainly Beta
類似検索 - ドメイン・相同性
ホスホコリン / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
類似検索 - 構成要素
生物種Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.9 Å
データ登録者Caillat, C. / Pinto, D. / Corti, D. / Fenwick, C. / Pantaleo, G. / Weissenhorn, W.
資金援助 スイス, フランス, 3件
組織認可番号国
Bill & Melinda Gates FoundationOPP1114725 スイス
Bill & Melinda Gates FoundationOPP1032144 スイス
European CommissionNo. 681137, H2020 EAVI フランス
引用ジャーナル: Cell Host Microbe / 年: 2019
タイトル: Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01.
著者: Pinto, D. / Fenwick, C. / Caillat, C. / Silacci, C. / Guseva, S. / Dehez, F. / Chipot, C. / Barbieri, S. / Minola, A. / Jarrossay, D. / Tomaras, G.D. / Shen, X. / Riva, A. / Tarkowski, M. / ...著者: Pinto, D. / Fenwick, C. / Caillat, C. / Silacci, C. / Guseva, S. / Dehez, F. / Chipot, C. / Barbieri, S. / Minola, A. / Jarrossay, D. / Tomaras, G.D. / Shen, X. / Riva, A. / Tarkowski, M. / Schwartz, O. / Bruel, T. / Dufloo, J. / Seaman, M.S. / Montefiori, D.C. / Lanzavecchia, A. / Corti, D. / Pantaleo, G. / Weissenhorn, W.
履歴
登録2019年8月23日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年11月6日Provider: repository / タイプ: Initial release
改定 1.12019年11月27日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation

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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
O: Envelope glycoprotein gp160
A: LN01 light chain
B: LN01 heavy chain
E: LN01 light chain
F: LN01 heavy chain
N: Envelope glycoprotein gp160
L: LN01 light chain
H: LN01 heavy chain
P: Envelope glycoprotein gp160
C: LN01 light chain
D: LN01 heavy chain
J: Envelope glycoprotein gp160
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)228,07126
ポリマ－225,34412
非ポリマー2,72614
水0
1
O: Envelope glycoprotein gp160
A: LN01 light chain
B: LN01 heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,9266
ポリマ－56,3363
非ポリマー5903
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: LN01 light chain
F: LN01 heavy chain
N: Envelope glycoprotein gp160
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,9266
ポリマ－56,3363
非ポリマー5903
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
L: LN01 light chain
H: LN01 heavy chain
P: Envelope glycoprotein gp160
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,1107
ポリマ－56,3363
非ポリマー7744
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
C: LN01 light chain
D: LN01 heavy chain
J: Envelope glycoprotein gp160
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,1107
ポリマ－56,3363
非ポリマー7744
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)65.686, 144.644, 409.405
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
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
12
22
32

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 102 or resid 104 through 210))A1 - 102
121(chain 'A' and (resid 1 through 102 or resid 104 through 210))A104 - 210
231(chain 'C' and (resid 1 through 102 or resid 104 through 210))C1 - 102
241(chain 'C' and (resid 1 through 102 or resid 104 through 210))C104 - 210
351(chain 'E' and (resid 1 through 102 or resid 104 through 210))E1 - 102
361(chain 'E' and (resid 1 through 102 or resid 104 through 210))E104 - 210
471(chain 'L' and (resid 1 through 102 or resid 104 through 210))L1 - 102
481(chain 'L' and (resid 1 through 102 or resid 104 through 210))L104 - 210
192(chain 'B' and (resid 2 through 126 or resid 135 through 214))B2 - 126
1102(chain 'B' and (resid 2 through 126 or resid 135 through 214))B135 - 214
2112(chain 'F' and (resid 2 through 126 or resid 135 through 214))F2 - 126
2122(chain 'F' and (resid 2 through 126 or resid 135 through 214))F135 - 214
3132(chain 'H' and (resid 2 through 126 or resid 135 through 214))H2 - 126
3142(chain 'H' and (resid 2 through 126 or resid 135 through 214))H135 - 214

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Envelope glycoprotein gp160 / Env polyprotein


分子量: 7481.677 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: Q74599, UniProt: P04578*PLUS
#2: 抗体
LN01 light chain


分子量: 23333.877 Da / 分子数: 4 / 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
LN01 heavy chain


分子量: 25520.502 Da / 分子数: 4 / 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: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 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
#5: 化合物
ChemComp-PC / PHOSPHOCHOLINE / [りん酸水素2-(トリメチルアミニオ)エチル]アニオン / ホスホコリン


分子量: 184.151 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C5H15NO4P / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY

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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: 4.63 Å3/Da / 溶媒含有率: 73.41 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1 M HEPES pH 7.5 9 % PEG 8000 8 % Ethylene glycol 10 mM Mn Cl2

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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: ESRF / ビームライン: ID30B / 波長: 0.9763 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年4月9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: 0.9763 Å / 相対比: 1
反射解像度: 3.9→49.63 Å / Num. obs: 35232 / % possible obs: 96.2 % / 冗長度: 4.2 % / Biso Wilson estimate: 104.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.144 / Net I/σ(I): 7
反射 シェル解像度: 3.9→4.09 Å / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3519 / CC1/2: 0.776

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.9→49.63 Å / SU ML: 0.4624 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.205
Rfactor反射数%反射
Rfree0.2606 1726 4.9 %
Rwork0.2179 --
obs0.2201 35206 95.85 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 123.98 Å2
精密化ステップサイクル: LAST / 解像度: 3.9→49.63 Å
タンパク質核酸リガンド溶媒全体
原子数14832 0 166 0 14998
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006515395
X-RAY DIFFRACTIONf_angle_d1.166721045
X-RAY DIFFRACTIONf_chiral_restr0.12392369
X-RAY DIFFRACTIONf_plane_restr0.00852608
X-RAY DIFFRACTIONf_dihedral_angle_d16.93415357
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.010.33971510.28722799X-RAY DIFFRACTION98.6
4.01-4.140.25551250.25752808X-RAY DIFFRACTION96.8
4.14-4.290.26871640.22812793X-RAY DIFFRACTION99.23
4.29-4.460.23661550.21422736X-RAY DIFFRACTION96.66
4.46-4.670.21751440.19892819X-RAY DIFFRACTION96.67
4.67-4.910.24751340.19542721X-RAY DIFFRACTION95.74
4.91-5.220.23251440.18522768X-RAY DIFFRACTION95.82
5.22-5.620.23581370.19262806X-RAY DIFFRACTION96.49
5.62-6.190.2621300.21032809X-RAY DIFFRACTION96.05
6.19-7.080.26391410.21542787X-RAY DIFFRACTION94.6
7.08-8.910.24581160.21452817X-RAY DIFFRACTION93.71
8.91-49.630.28481850.23162817X-RAY DIFFRACTION90.69
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)
11.143559624790.5192214140790.178659790231.09189903829-1.083744288261.55146008469-0.3494828874980.3409415594580.3536655690060.5669759910910.499733425825-0.4476635136880.1071111071170.448477611423-0.381615990641.78878087745-0.637524633142-0.465566219383-0.374055033006-0.8895865055730.794653709726-15.898198226546.8866386448-60.5463508778
26.087751264333.84623560586-1.566939821288.774491180190.004196797551195.383025926480.351047891421-0.79194682780.4258058981940.955376524518-0.7497972468311.20042910210.6254170319560.5887984827270.3087120332671.43282732588-0.333217183562-0.1794725604870.99128087110.01826251708350.690857044881-21.02055233534.3573696515-52.4043585443
37.17197489657-0.144030816469-1.622457622576.95635237413-1.978364662312.007476492190.0593312877758-0.693667661361-0.6747220949842.13655938768-0.430369233592-0.891433309423-0.1185999638882.591531601310.3993401050691.22305490737-0.1999608172480.003463370642530.9034267847480.02842079019420.985877715579-18.567377816716.173571403-61.0758404989
41.997128975990.300729767698-1.420695850936.951963128170.1878525637162.477624194830.434933551754-1.000971494580.1110444695862.41160533976-0.03146591710930.6414192394240.03039121052190.514613002405-0.2919726839461.84105837941-0.1731990916940.2706258063881.145425924070.05877700181020.915350540848-19.951429792159.1680074205-41.0021277984
55.42770183042-0.650632533729-4.342940228335.347097827773.208407969495.907005643530.4933934562860.2084907771441.99969873142-0.7852503407870.03103997046960.1327223568740.2688302424290.410826336288-0.5158734361762.10044098144-0.38263689520.2500823047141.57952480088-0.07590119050581.54568705267-13.184565299594.534340438-34.284134559
61.260757716321.08779091837-1.758901412043.29568141829-0.6806295412032.597822097051.14616287223-0.319737600504-0.2205781916770.265671550835-1.89085949528-1.190087267460.5071636646140.7222769607250.7106596025411.2267489265-0.14554748601-0.1089980949531.050549899210.1234979370181.197550010521.5192041973163.7059747422-55.6171848458
75.729381990321.287064027580.6519262103446.66483810746-2.063609552898.20722255460.0782898850444-0.0232823475137-0.4309186044570.852739560483-0.1294167367860.4003992772561.07953192675-0.5609925865410.0544365830781.481809634310.0555405155416-0.08206079195780.841347555165-0.05366804821771.0463965025-8.1977281533359.907598317-58.9969203739
81.002710604432.148733774740.4351822272764.53416864697-2.14881218511.680013910870.3792557022360.394636990151-0.3019693021270.240929266188-0.109947221651-0.5378237956910.485858047674-0.238778932884-0.259495706731.642882794050.00190430826898-0.006545519532310.956715002765-0.1002722009781.12282353647-6.2973338505558.0345721718-53.1103900484
93.6459018755-2.2296447414-1.469285134953.04606024062.969294750893.61723574633-0.446071472454-0.740827717841.44394198481-0.6261829024660.2627027009260.644228705003-0.257747375441.300039759470.1803068581111.75731530911-0.7093223972170.1800546887481.54122410453-0.1716487762081.18306850666-0.11133648865990.2623443851-47.379730803
106.53487742213-0.563136422584-4.065821516634.90696793977-1.274146388616.013601256150.19837600467-1.602492612810.767146124366-0.4726557005520.556274497308-0.2773311382890.8613059127421.00855385889-0.8361465537261.6945358457-0.2649198981880.1002867550821.78147679537-0.2709771225761.203530846020.43510958256487.0236360312-37.6159168524
114.51818461799-3.921783039132.788654437574.50635091351-0.8084431336874.061597384730.2665343695532.434422299962.36464154569-0.2679756943540.136271977849-1.15341101324-0.4089534654431.98710272364-0.0827798600231.83716454256-1.136668095820.6886517426812.07461180648-0.415387520352.089258659858.2191804765892.7933634993-36.90477462
125.20104803409-1.541782339634.208996537893.338431338580.7134801935137.100698311270.343616993945-0.342209873052-0.41384827299-0.304417438818-0.05610823529240.3696687339651.91758127146-0.181152577176-0.3306178531051.11459055823-0.0007315563886210.1066266438530.8998917431980.387481948041.22085645148-35.938532715512.5543061143-89.0273490078
132.77963905393.208389967923.543554707117.026072931765.720115230067.668822237911.54721948061-0.220797310936-0.3071225342360.761300564097-0.323537130755-0.8794471603720.7976321221341.22297542583-1.305458301681.35968254021-0.0400602490326-0.1397015210971.062592548070.1331288561621.5223819081-42.60746364061.40379195579-106.856433782
144.345186423312.88511435078-1.974131662042.987123118240.5836267008348.000223977440.1314413542520.234451224955-0.3914606913860.2545570855860.28901646174-0.742150708217-0.4577956635170.195073199724-0.3504379060481.0042345450.292470184647-0.05823596079760.6957231978630.05947988822231.37105674413-39.17900360859.29978094871-126.838732153
152.703590366572.870724568150.772385412894.57436195321-3.072464409119.869523342-0.127004019418-0.4887820685130.3374923204440.1168527487940.2632755266310.107116426787-0.522809939894-0.0101240474425-0.05540259599211.048986882880.3927480137130.1485475151440.6631124322910.07958156042620.826207936301-37.627348247233.7530904729-95.0286828889
161.92798900790.1281136174241.173904156543.91466230121-4.717056293128.687641523280.189380664219-0.09603483001280.5307641142450.7548162227530.09251820307480.0966543024673-1.04354599097-0.0737648818664-0.2325190531760.982648949345-0.02133215919370.09448173324310.7433772682450.1466637789360.993238605135-34.832490320433.1937564615-93.0302234391
172.975807989391.566515047670.5435372430113.706078340670.8662424895016.368790664450.08966981999180.3845861581180.498661457090.162679769521-0.4996266407190.188174744994-0.5399876784860.001972849528320.2950497956350.9711371098310.165892028359-0.02315533889820.8848247674310.07547655845270.956040205477-50.288357693519.6625740477-123.538259774
181.854585787140.730146710877-0.395893952186-0.0645010970838-1.170512992041.709460341130.497862408691-0.537497697712-0.4779200957770.0581785694606-0.01704788624680.4253182360170.423080507405-0.785364196849-0.08802736830891.82965405629-0.258110410151-0.06841912467040.9021244987880.2317759130760.881837545028-28.602088456821.3742854745-56.7347901056
194.527851951530.971071530372-1.719886776197.7964955302-1.349444371577.803625754940.3070819056560.37536619937-0.06278300859490.469249120978-0.388494489172-0.595988938863-0.5430114051860.7722915352920.02873646264660.513704347681-0.132325584077-0.03277793437990.7277735182980.02946106205050.748924339542-51.1294425223-2.3101079255-19.9647642172
203.940756837412.33875807737-4.351361041981.9076011045-2.882705707544.904644516430.14930565646-0.9077926290390.360455903073-1.148843473680.549345037320.5786056597580.9416149493112.61548465455-0.7525109160671.15936132864-0.192861974181-0.1372051259031.09237458902-0.02181949106020.835248611328-56.3823959972-8.055623469120.278177588695
210.2541289570461.5087599631-0.33323132727.239267465410.6292227764644.43252695-0.212894487157-0.0984092476252-0.2196018442010.04532051566340.07705019670520.158943698944-0.2420839773540.2194981641710.1634293965010.258023192442-0.02083315742380.002477247791461.095951302070.06080372082960.748429483934-59.2453897877-29.24468671846.20841536209
222.44901768347-0.379550293367-0.7348216808579.369465381091.145423516984.728942163630.1418336814790.1205945801280.255111782040.117698081208-0.1650440688830.096141497289-0.0324624057532-0.171619080869-0.05852638501340.494600087989-0.0668673799370.02353527701010.8612180883180.2017016095240.714264414729-59.9214730934-18.4098344488-32.0322268779
233.53426367353-1.88019042278-0.4610575133139.437188442820.145649710333.986986017590.4098025120950.6130035526040.199324577559-1.07410247431-0.494888286781-0.485607954617-0.0774928127991-0.09454394012850.110423801630.3789173665270.1176518942220.1111145055370.706451535070.05910949292930.554804626552-56.451512103-14.8345473415-35.2259023131
245.799021460051.00891058566-2.568153106951.28082181474-0.08138113803267.58965205305-0.5704339900740.137009400658-1.06284592452-0.528605208424-0.7891121399250.925031690822-0.322595566171-0.4830938284070.629873361947-0.3336286919210.03373969561970.0364334047280.830597216170.3292854056551.25793217886-67.6465243393-32.1619196774-2.94226983934
253.39643552696-0.605436319473-0.5022957491887.022714064042.219543370375.821821083910.0969367334879-0.159467612519-0.285463967179-0.196565143516-0.02353619894190.294769818853-0.213507961031-0.317723670294-0.1600543653210.329218188345-0.0885308798224-0.03269905060461.256287079630.2085541493490.81186699446-72.391336461-28.5868297677-4.21458763245
262.013099553095.587919083712.017049652126.75198270542-3.139094964472.001844354951.48370291616-0.05896024677973.012537713031.167995159260.4684905259051.29835757203-1.888523772720.672412647784-0.4829425116870.506476915363-0.440042551807-0.251597425340.8064140359960.270217939369-0.117583808113-40.0363898205-16.7763663307-45.09675918
271.30760949941-1.133129383321.990532346255.0356088139-1.528446574442.55612170432-0.500089254911-0.393134343167-0.119220718490.9736273053341.066931265820.165306872628-0.7199852588170.221528788344-0.7703920976831.340705547330.04467531722410.3684317455190.9085688551330.2301774103880.985813643541-44.84369604914.84300907644-44.5277269243
284.18974871003-3.32929341129-3.463517451293.420145686363.288447999353.49589078191.313699953732.624812123922.6843307308-2.349737848410.7863006933570.0207187912594-2.129619688050.00661577263677-1.556166104231.26738098133-0.3556375661870.1827922468531.591747039960.2339013382711.21782494804-39.959084619212.2263158501-64.4733795918
296.90047673207-4.67898844761-2.820387906115.19420984349-1.307537584925.997136298290.2522433718342.33058546989-0.638172803212-1.84060700756-0.484139593079-0.537229780853-0.0704229458563-0.9576105082610.2587744232021.296426558990.1207721898790.01950816811010.796911538218-0.02815590303670.701637238186-12.9009838667-6.81301533475-80.3665395822
306.58085230621-2.016034360211.169842981734.55221986709-2.466724933299.09301350204-0.163110153251-0.544574180854-0.507362412804-1.314291446290.04515522598830.1002933790160.325612568466-1.845536495980.0405923872420.795817269303-0.0215736244750.05307699211840.595291918864-0.1020993279510.855508755197-19.3017970033-4.57550030517-72.9880177722
319.324250352183.85723988477-3.164063777478.6736347290.3468382425262.22897880731.18335190909-1.280727755550.9886382392030.798544003979-0.744965999719-0.359539187914-0.05279527830180.738185062969-0.6070300041481.07371535488-0.07340382662520.04685989330610.9116879068160.1725482463520.790315934104-8.93298051315-3.13747050121-66.3097761656
321.937246839130.4923871639040.08138318479456.449688532580.9333506506032.340028055930.0749107683147-0.610437166159-0.0148928214626-1.155921525980.0169062430424-0.5308886820320.3545218455940.2758937634710.02503272437270.941600729746-0.08564407530820.1858786396520.7521250479270.1402380891130.811658840726-10.9408053858-2.61986188518-74.3301373856
332.71803108569-2.030027686631.097680286638.945288415991.003571254476.90705859558-0.1650021874390.0655282411020.65505117383-0.2929864792110.08475253426340.184596344217-1.02193378375-0.5517740562410.4668355110690.626136871672-0.0851468286803-0.1362788129690.9500684523040.3672966718150.602273716806-23.8241483407-11.5820723525-68.9848420077
347.74413584859-4.69468415442-7.608692301692.862309267744.661403621438.583904506690.07007709980642.467494598160.300293332275-0.926521416641-0.575775925629-0.4300476548690.338332390586-1.988077000970.189021927551.00295782359-0.05458926307240.3316963803681.232386784530.1658780335071.027624294651.47077020407-10.6812084814-86.6475518932
352.986072124531.3760810329-1.547593502775.720521757371.563800189035.464331154690.3225536121160.463146168599-0.305604812435-0.3215937475420.0755432414211-0.935098678793-0.118640239243-0.259163094307-0.3221777046010.952495973499-0.1041957906410.09609292006310.817419519115-0.0450957479861.044368509025.63789322544-32.1220961663-89.1346037829
364.393367298853.45040356985-0.4712895407577.35206216029-0.3119876732562.68373184459-1.009632238340.7095169347771.23069554002-0.8277180894810.7617046507381.86761671937-1.140064574712.747467158630.1698911670840.852552057911-0.117260230638-0.06775280905631.44849868173-0.01554389943860.917917492594-2.47532063928-34.7947495203-92.9542473186
374.262214185281.72801018021-1.488223325062.01486363394.3351789858.752446105360.561700082591-2.59884246210.2293102263440.02354310086870.852660163738-1.192705820322.95376222470.898903971363-0.7135033840181.51930189834-0.3204092691640.4711510077651.23321636647-0.04077691677751.2416324365.58164025047-15.3398888611-81.3935597883
387.61617699668-2.23542458577-0.653537417372.87279140483-3.332007690415.664961372260.293281407758-0.45106106555-1.35818372055-3.5427061682-0.122195310206-0.07056292353942.2697892078-0.591222964103-0.1079384321262.0132130080.0134245562937-0.08308335604021.1130425339-0.1883933152781.239767740342.44525405133-42.24484984-90.0670500967
395.27028559335-1.0159705927-0.9885969529896.063855689380.5670057344011.61666264206-0.1459554115220.497802758459-0.628549018112-0.3662343129550.2700682725131.53450722045-0.6916829422040.0210595033531-0.1086970842341.355491856470.0959547981070.1889339148580.851857315147-0.2545224847190.6058433265296.08394785359-31.4785670552-98.4398633416
404.100836151961.403748800111.759961016818.41350515594-0.08880123803832.98863494347-0.06939832229760.157203165506-0.619966390331-0.3881814861040.1453440632540.03412053245810.6746325047170.368525207028-0.1259721058550.823585172516-0.09761510053810.05964040437460.7536848286330.1042894623350.639823423567-14.5738112278-21.2110159318-58.0763420308
414.563037759350.473501218614-0.682730963646.54412655503-2.151078570372.72791144302-0.157764944432-0.316908536692-0.479115980343-0.2749617991510.4170185279870.9478300474320.336444401601-0.741374157489-0.2342203208090.578131641522-0.0430121392431-0.02564998609130.7862905362520.02034785184130.711078948824-20.7070371826-17.4638627024-56.7576308613
421.70183816472-1.62971845495-2.181507641352.675411498371.614718395812.39625002278-0.277321904068-0.277532053903-0.1575599500770.1362493302550.401660366723-0.1139310682780.4398465214420.494691327116-0.2239797787140.8920843771610.06124098426990.0185327611030.95734238966-0.1352467479010.778813987168.00360842141-31.8230973242-74.9264800107
430.592750122257-1.48148497508-0.09757613142757.174074922691.296518995092.379888317291.278562800531.38212497778-0.0975059291119-1.18116350944-0.454354838631-0.41079435382-1.288042429920.804691075291-0.212841237870.993595239657-0.1630640930490.4830189335780.6162078705220.3996323296320.766878314024-34.52327781086.29151056377-55.4359653582
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'O' and (resid 671 through 675 )
2X-RAY DIFFRACTION2chain 'O' and (resid 676 through 692 )
3X-RAY DIFFRACTION3chain 'O' and (resid 693 through 709 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 210 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 109 )
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 134 )
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 203 )
11X-RAY DIFFRACTION11chain 'B' and (resid 204 through 215 )
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 101 )
13X-RAY DIFFRACTION13chain 'E' and (resid 102 through 113 )
14X-RAY DIFFRACTION14chain 'E' and (resid 114 through 210 )
15X-RAY DIFFRACTION15chain 'F' and (resid 2 through 52 )
16X-RAY DIFFRACTION16chain 'F' and (resid 53 through 119 )
17X-RAY DIFFRACTION17chain 'F' and (resid 120 through 215 )
18X-RAY DIFFRACTION18chain 'N' and (resid 670 through 710 )
19X-RAY DIFFRACTION19chain 'L' and (resid 1 through 101 )
20X-RAY DIFFRACTION20chain 'L' and (resid 102 through 113 )
21X-RAY DIFFRACTION21chain 'L' and (resid 114 through 213 )
22X-RAY DIFFRACTION22chain 'H' and (resid 2 through 52 )
23X-RAY DIFFRACTION23chain 'H' and (resid 53 through 108 )
24X-RAY DIFFRACTION24chain 'H' and (resid 109 through 135 )
25X-RAY DIFFRACTION25chain 'H' and (resid 136 through 215 )
26X-RAY DIFFRACTION26chain 'P' and (resid 666 through 671 )
27X-RAY DIFFRACTION27chain 'P' and (resid 672 through 692 )
28X-RAY DIFFRACTION28chain 'P' and (resid 693 through 709 )
29X-RAY DIFFRACTION29chain 'C' and (resid 1 through 18 )
30X-RAY DIFFRACTION30chain 'C' and (resid 19 through 38 )
31X-RAY DIFFRACTION31chain 'C' and (resid 39 through 61 )
32X-RAY DIFFRACTION32chain 'C' and (resid 62 through 90 )
33X-RAY DIFFRACTION33chain 'C' and (resid 91 through 101 )
34X-RAY DIFFRACTION34chain 'C' and (resid 102 through 113 )
35X-RAY DIFFRACTION35chain 'C' and (resid 114 through 150 )
36X-RAY DIFFRACTION36chain 'C' and (resid 151 through 163 )
37X-RAY DIFFRACTION37chain 'C' and (resid 164 through 174 )
38X-RAY DIFFRACTION38chain 'C' and (resid 175 through 188 )
39X-RAY DIFFRACTION39chain 'C' and (resid 189 through 212 )
40X-RAY DIFFRACTION40chain 'D' and (resid 2 through 52 )
41X-RAY DIFFRACTION41chain 'D' and (resid 53 through 100I)
42X-RAY DIFFRACTION42chain 'D' and (resid 100J through 215 )
43X-RAY DIFFRACTION43chain 'J' and (resid 668 through 701 )

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る