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- PDB-7tuf: Crystal structure of Tapasin in complex with PaSta1-Fab -

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基本情報

登録情報
データベース: PDB / ID: 7tuf
タイトルCrystal structure of Tapasin in complex with PaSta1-Fab
要素
  • PaSta1 Fab heavy chain
  • PaSta1 Fab kappa light chain
  • Tapasin
キーワードIMMUNE SYSTEM / PaSta / Fab / Antibody / IgG / MHC-I / HLA / peptide loading complex / PLC / antigen presentation / immune response
機能・相同性
機能・相同性情報


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP1 binding / TAP2 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP1 binding / TAP2 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding / protein folding chaperone / endoplasmic reticulum-Golgi intermediate compartment membrane / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / phagocytic vesicle membrane / peptide antigen binding / unfolded protein binding / regulation of gene expression / ER-Phagosome pathway / protein-containing complex assembly / molecular adaptor activity / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum
類似検索 - 分子機能
Tapasin / : / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Jiang, J. / Natarajan, K. / Taylor, D.K. / Boyd, L.F. / Margulies, D.H.
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: Nat Commun / 年: 2022
タイトル: Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation.
著者: Jiang, J. / Taylor, D.K. / Kim, E.J. / Boyd, L.F. / Ahmad, J. / Mage, M.G. / Truong, H.V. / Woodward, C.H. / Sgourakis, N.G. / Cresswell, P. / Margulies, D.H. / Natarajan, K.
履歴
登録2022年2月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年9月7日Provider: repository / タイプ: Initial release
改定 1.12022年9月14日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
改定 1.22022年9月28日Group: Database references
カテゴリ: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32023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
D: Tapasin
H: PaSta1 Fab heavy chain
L: PaSta1 Fab kappa light chain
C: Tapasin
A: PaSta1 Fab heavy chain
B: PaSta1 Fab kappa light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)187,4548
ポリマ－187,0126
非ポリマー4422
水95553
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)117.422, 68.988, 142.981
Angle α, β, γ (deg.)90.000, 108.415, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

#1: タンパク質 Tapasin / TPN / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


分子量: 44739.641 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: TAPBP, NGS17, TAPA / プラスミド: pET21b / 細胞株 (発現宿主): S2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: O15533
#2: 抗体 PaSta1 Fab heavy chain


分子量: 25499.457 Da / 分子数: 2 / Fragment: Variable and Constant CH1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pET21b / 細胞株 (発現宿主): Expi 293S / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 PaSta1 Fab kappa light chain


分子量: 23266.652 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pET21b / 細胞株 (発現宿主): Expi 293S / 発現宿主: Homo sapiens (ヒト)
#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: 2 / 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
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 53 / 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N

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.94 Å3/Da / 溶媒含有率: 58.14 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 10% PEG 4000, 0.1M Hepes / PH範囲: 6.5-8.5

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データ収集

回折平均測定温度: 273 K / Ambient temp details: LN blow / 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: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年12月14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: 1 Å / 相対比: 1
反射解像度: 2.8→47.45 Å / Num. obs: 527753 / % possible obs: 97.65 % / 冗長度: 3.8 % / Biso Wilson estimate: 51.18 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0871 / Rpim(I) all: 0.0517 / Rrim(I) all: 0.1016 / Net I/σ(I): 10.44
反射 シェル解像度: 2.8→2.9 Å / 冗長度: 3.7 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 5107 / CC1/2: 0.483 / CC star: 0.807 / Rpim(I) all: 0.8211 / % possible all: 95.32

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
XSCALE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: 3F8U

3f8u


解像度: 2.8→47.45 Å / SU ML: 0.4639 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.0802
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2742 1997 3.79 %
Rwork0.2312 50732 -
obs0.2329 52729 97.68 %
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: 69.1 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→47.45 Å
タンパク質核酸リガンド溶媒全体
原子数11261 0 28 53 11342
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00311623
X-RAY DIFFRACTIONf_angle_d0.642215987
X-RAY DIFFRACTIONf_chiral_restr0.0441838
X-RAY DIFFRACTIONf_plane_restr0.00692055
X-RAY DIFFRACTIONf_dihedral_angle_d14.1811651
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.42111380.37393502X-RAY DIFFRACTION94.72
2.87-2.950.40781380.35833496X-RAY DIFFRACTION95.86
2.95-3.030.38781390.33413569X-RAY DIFFRACTION97.17
3.03-3.130.37631430.28913607X-RAY DIFFRACTION97.68
3.13-3.240.30641410.26633622X-RAY DIFFRACTION98.48
3.24-3.370.26621430.25473616X-RAY DIFFRACTION98.12
3.37-3.530.30421430.26123622X-RAY DIFFRACTION98.41
3.53-3.710.31011430.23963650X-RAY DIFFRACTION98.7
3.71-3.950.27821440.22963653X-RAY DIFFRACTION98.39
3.95-4.250.26451430.20853618X-RAY DIFFRACTION97.49
4.25-4.680.23181430.17383644X-RAY DIFFRACTION97.83
4.68-5.350.22861460.17483682X-RAY DIFFRACTION98.91
5.35-6.740.24421450.21483692X-RAY DIFFRACTION98.56
6.74-47.450.20671480.20473759X-RAY DIFFRACTION97.16
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.07528693483.176282338751.613498933345.32131662631.991468639513.62938580613-0.1931118353810.3319650031580.320680796964-0.88709686745-0.2228687292320.6843745152820.441428408305-0.864188542720.3681419815860.6755271313330.00528916675242-0.07943244769970.848292851719-0.2349581632760.616632209244-7.7117746451538.82621528734.88511877295
22.70775683545-0.364843852199-1.599574233122.32241951270.4971366096155.66733925957-0.3622325234080.200652514629-0.353476280042-0.172024669124-0.2804127877470.2241829742190.462658942131-0.03112707809360.5660155875860.437489807717-0.03844865754140.1036193180750.265685478797-0.05388890737670.409266857228.9173000303537.959738350810.9454176029
37.24554363396-1.74059717196-5.431396569542.110858346852.298363358515.92869549891-0.361536174439-0.369350174541-0.4815330957750.09507035004380.154166867470.1330337522570.7332950663540.6209379205090.2423910513010.586668232518-0.006476372809570.1125458809110.405941044151.80583972222E-50.30730056238116.843542620937.727027456110.0123753699
45.50163471618-1.970912489070.8186275768874.272019890820.49883435141.61767855834-0.2139332047810.3673427858420.350785593368-0.4104238449240.0507865048365-0.2857974809040.145037100888-0.2845298855930.2271408337270.769287067075-0.1578949707520.2548305845780.787740932071-0.07166345012220.38768150468728.926108478240.3954485715-32.8750555973
55.453850188163.043955343714.610157911084.388774744014.027976849325.58819331364-0.41703828031-0.394611216897-0.0455548702793-0.00882958173224-0.329389248060.3335310133140.833052280731-0.9045656626120.3829603904070.530350185208-0.08252155539730.2546482680250.4992624469320.01481537066670.333714889434-5.0265963480647.266565082550.22903908
62.63201871146-1.76218443118-0.404594892.56511031738-1.093908875634.19758831339-0.27214215913-0.171099205008-0.2535375247190.659725601475-0.0911752940514-0.04915574835330.470681062201-0.1083382700570.2451885419110.210652715544-0.1278836640.1192631731230.366278268398-0.01246563484810.2779031514932.7630725660148.677205153946.0879477295
73.16810188884-1.09665843687-1.161684386832.096959653581.29960105790.872573208359-0.0359450428632-0.5904002700170.2150823765450.1965200790120.376675359019-0.0425040333849-0.642535594778-0.414361029536-0.2107049129530.6269806095350.01564827509570.1708888175340.629269673770.003259584530450.292948609085-10.428661467567.324815579161.3281673285
82.92575884216-2.117181526710.6722387360134.987630261140.723749835373.2117533477-0.210525767895-0.3486477848510.04729076331380.664903323330.2406097940460.3912493385490.105769783403-0.5175295226120.008618055662520.5546537613640.1192271066410.2030782111560.719215276396-0.0039086041510.357456443866-16.435154017170.528595795164.2016195332
93.49139828444-1.16485291726-0.6961782274691.36871675424-0.06135333275471.850621339120.4847544691650.180476830270.5283529823010.116724751661-0.312099402451-0.209414450953-0.574738931375-0.0517033731191-0.2072194807670.565602166312-0.1018810255880.2378409192420.355473338512-0.03404041771940.429947139123.3237151109272.250829390633.9334563293
103.0723217468-0.974541375327-0.166601483476.951649130180.2427904845775.865265961390.0852612674220.241172842586-0.0118508503371-0.110496617507-0.3307041195990.267872898564-0.618452409878-0.5591710542660.240926945390.3297937759690.0414541382960.06163845967680.396496037548-0.008711610122090.265625656669-3.3501480676764.978902422932.604965294
113.2319406683-1.93583518593-2.033022563564.20403166962.453744548613.991294114990.635372891495-0.09772016462030.480256310418-0.250944424733-0.127913263786-0.615476277386-1.20916346815-0.251004670962-0.3669088501410.3455078231240.01060956216740.07980767329790.325245258512-0.06634997956340.331730351238-0.00450242196469.973282759340.1779887476
121.23663870943-0.1463449202580.2251220741570.44337067647-0.7094907521051.14281517007-0.36436123265-0.768165512489-0.005203511918170.9483512793940.159419818680.02408478430950.615243048802-0.061073891649-0.002463944892451.010620704860.2980344708220.1131577358811.12499004788-0.4198657353430.260930867696-14.391194636679.488719985872.9308590014
132.38290151813-0.5316135706350.2373675866311.39160482402-1.474175620084.97873963006-0.150136469941-0.3043702905550.5873590650870.3247471747290.2521697464-0.608597562244-0.2398735205870.511758809114-0.06522904863980.9492583852990.1171965104060.09301888158080.548684704923-0.2174029026960.604824452435-8.0454872027284.344185068758.660773791
140.994253232272-2.25449259148-1.42477730295.11874645553.150048072248.50541467223-1.11372553138-0.7836930269230.8826164177680.6096380577960.561790945931-1.157608142670.08643096844960.734247416318-2.271101413150.9879970769570.333093939618-0.1867909380061.26585412909-0.7326023901560.804461570059-1.9060374854185.921944405868.1095393146
154.508577695213.253163741762.636279091172.507681340612.35659121352.801212898871.124616325380.178753656768-0.1705596922260.41621301598-0.267859563765-1.65232623304-0.09029796880350.0495261101714-0.8633726571070.9204687702340.0762872456930.2096647364370.1894024867620.03273364780390.826642600611-10.831812518878.600564191647.5524191331
161.302717109340.3948248775020.2925738937760.5281144275680.8895326651991.60987005243-0.0942054556482-1.134736371070.7970688687621.066424656970.957983567366-0.786054549402-1.182466548360.985242645515-0.7690079369251.404975752440.2632258679530.02354061298561.03878788397-0.5274699937520.910789547839-8.6077054329988.318959659669.8758596117
173.7438335191-1.01388192798-0.8546259221046.41478610615-0.7045593057291.04499831492-0.484596717151-0.8942001369-0.4557003111851.03167012417-0.234224103377-0.6415209939330.923961140411.541564367960.5456439045011.098202638260.3833314224380.03851067085351.522940130460.3523614517740.71514075746442.067485968732.915445905558.3946529628
183.596638824630.723809212806-4.790270521270.361468859748-0.9878199224176.66347705676-0.544876805552-0.40214505563-0.2706730285970.05616353182490.0708828090221-0.1319180185840.710935795020.002853668513820.3836593840750.6613782699420.1369935246040.1336223329450.5163358353650.03753746877280.32179322501421.137707501835.275888245956.9013877636
197.56909138556-1.06204502727-4.572010772454.041833860361.344145525763.87954338316-0.124000681975-0.03905048323680.2828783253310.4814132426370.0887106223076-0.05172549486250.517264349475-0.108834125650.01416514064940.767310860080.1595491739460.06645893144210.744136246213-0.004050013691220.3855909981715.4054265527436.701410286899.0563075968
207.53737389022-3.006183613458.388072122243.04027790576-2.951067981429.38864916759-0.4045223723530.9122888034840.24181113058-0.233188634251-0.0689699981108-0.483724783498-0.184244065980.09753161856090.2252587855450.1896175172820.1073524630990.1364518526830.46503675468-0.005362871072060.48206730684538.016930214752.008277134910.3227125766
212.643842638431.82184870758-0.1425957239353.051768190641.120463808736.09395206859-0.1420245471140.173110504401-0.203682712591-0.2064916317240.047237719019-0.1584267145720.268855043792-0.06317807067940.04392400833730.1979746996970.05945207057340.1314406691910.2114581167930.01344115882690.25534542813933.805580810247.517276368420.7226189272
222.872787115561.077641838092.587437096023.10704233409-2.707762818967.30066778737-0.597744725386-0.461565566803-0.205855936338-0.1788720280940.6260009724440.09755818006030.0342968056901-0.381490240584-0.1447636165870.3447511364530.03597151576820.2094611261470.383170813674-0.07838216385050.32727869855533.078160130148.147078866512.3988916853
231.989258503260.935835054634-1.100259768882.77063097578-1.883794678333.53822989184-0.07442942475770.2614599994980.193636150229-0.3749941356020.022492916879-0.513155309945-0.247274404050.08722630302710.258350073260.462077725075-0.01810160625490.2861299112530.247282344859-0.009570113064530.53542322340443.24892623261.855659936414.838039938
242.002621184850.5799417320023.744974514525.14777536413-3.946894923724.74531338728-1.481634066410.2109819984120.752454552422-0.5960871901420.378121629501-0.678082617955-0.184656873743-0.3531219050290.7609638270560.697350761411-0.0260888258630.1561435109190.702291809239-0.05369506113070.45267456963749.687324972174.48801927462.28991997298
252.220618437392.317914927583.851501393044.936640741862.605622353327.442772690340.261818717615-0.638723067947-2.53746844736-0.2039443215360.911190443046-1.626373869820.598369721686-0.137535499274-1.168257459810.745959112171-0.152219361308-0.05953194319180.3513850715970.04114317004841.1677302910849.99792974466.03999691226.19836033904
263.127819540630.976869088689-0.2008669372512.985878117182.107202388182.21513086662-0.08076534613860.006188427958090.518493175091-0.02046174558270.0659176390622-0.280622408757-0.5065305823850.3013222710480.1560027249010.641581840151-0.06370121362880.2158012077640.3315489715860.1063839256490.61102594786646.62974559872.67289036648.35821749515
277.07134787480.680663642803-2.862392266583.443895382840.7752176490037.137299194240.06011984334-0.366226755181-0.0839191085932-0.2898266831130.0759168156338-1.053233407870.1120376832211.68601129959-0.1636559444590.827981574570.0006843959069390.3769146650120.6657754161460.0240595689230.84892915369957.20041432773.82472882745.17422312557
287.183475926792.31869672924-3.2574831461.65585847847-3.506508344848.0996210034-0.06675304460790.693965942927-0.472614987771-1.95740410815-0.329752048964-1.123282286540.2208834445830.5502196885110.1745088821341.064382459590.02864577772350.4130569008730.517522758821-0.1237616435641.0597850471455.042035545568.3254887821-2.32425350328
296.479656303094.38877680933-1.251906005117.31982588579-1.4535498151.877966868960.733142222342-0.2590765419410.438912091260.74966925838-0.30694574743-0.0252852118285-1.10979574150.007592581385-0.3965166074880.8433538603290.02263550525570.2793042220940.350299144729-0.0994581315930.45341475874633.662790664870.667596237235.5831502836
301.36433441217-0.829250121650.6311116577385.17784257251-3.16018683422.86845486587-0.0616467899961-0.0475152790889-0.219317282785-0.0877119319175-0.629592134286-0.708617923456-0.5925570404560.2558251610620.4449551876630.226701581003-0.09096193247380.03955115107250.289291506349-0.1802311283730.37734026169837.982539854960.452979204932.3135536298
319.88433167155-0.656309483167-2.207896853012.91856088543-1.589270171333.84660287171-0.0240150843436-1.006196809410.3652431347710.7070520774490.0132781785442-0.185650916565-0.3724384839560.4826639027940.09348521108860.733676536533-0.01887799907580.02134599974570.454524955733-0.04555924171110.35177683047640.914780129662.356022695140.657883136
321.839834140611.20103553688-0.8512569626163.11519764256-1.608872688321.730765677940.3253877184390.02419360995490.2389676688860.210004743251-0.232301408973-0.148816663553-0.8501243398090.178734715463-0.05285038481080.753515998922-0.0470209455760.1008596014150.227482709213-0.06218925673080.42418610710539.471151266968.759827213230.6112335129
333.01454095641.08357604624-0.9963856119592.49841966151.207201668281.50717712946-0.7274947751670.576836004853-0.713375885089-0.4680611717840.0628976437363-0.3666502167620.4284645513330.001851729430790.4832409745621.3678217593-0.05131921005810.5803127741280.3615925799340.07415875310010.84728203701451.105126281682.1304470301-2.75116993605
344.45077237848-0.08065980906561.902204697665.29376942918-0.4587657311353.04866673064-0.523771203668-0.163417626285-0.223764804327-0.5775708027160.67776659124-0.389651022769-0.880591324941-0.692859533054-0.07429134624790.8444937624050.06472374015330.1953662954440.359509873680.2213540097170.75684750988445.196624068186.453856195410.5204054277
356.55064538851-3.487375375224.707299531047.82303331817-1.273239009393.639440111910.2267242226580.306504549911.15193515536-1.72537283177-0.1792906134510.4401036226081.15418373291-0.3445199874110.2139841923210.8821183265410.08719022111280.111824608930.7040803068490.1647505612080.82242288720639.161082129387.4539427444.2265268855
361.8452824601-0.7516262158740.134925980784.17203247002-3.382283635472.872887091160.0563477893285-0.208191412288-0.3061027001580.304620928439-0.3133504453650.4571732369630.346456420309-0.0584654917219-0.2011554224481.02044667082-0.2027767011110.1405807823820.0342796190066-0.07795213865490.77184472111748.562790432277.396093694422.4496533547
377.503991367180.995674042927-0.1802710907524.781582700153.971404375293.43809131165-0.579165560421.106483431740.801502201852-1.12736179072-0.1263230513010.837793445058-2.744318067430.1370400886820.8437859419681.42949252677-0.09096271675860.1659145165510.4201856631120.1942708774630.82390164509542.37241986383.8871916026-1.18014453617
384.34461211743.120064841733.616025301552.243279102742.59744639893.01116612404-0.8400947616760.3736364032150.82439509766-0.928197667379-0.3890396144360.0221295304043-0.473766033563-0.1792159033231.031657658881.889309223160.01476048530480.2043334953780.8754439051730.3439749832041.0190211783345.46974892592.5878021829-2.2209895243
394.73624770404-1.440521716252.120964728180.959848919484-0.9633484851035.94971509409-0.1795003625990.08535832824810.516658743805-0.6908759531470.446180417394-0.775065529649-1.969387997821.11888944518-0.4110583720061.24382686825-0.06676737393430.6463452975060.576903994414-0.0857475537620.88409132749149.91450354194.35496588368.06735073077
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 'D' and (resid 1 through 109 )DA1 - 1091 - 78
22chain 'D' and (resid 110 through 199 )DA110 - 19979 - 161
33chain 'D' and (resid 200 through 269 )DA200 - 269162 - 226
44chain 'D' and (resid 270 through 388 )DA270 - 388227 - 343
55chain 'H' and (resid 1 through 34 )HC1 - 341 - 34
66chain 'H' and (resid 35 through 106 )HC35 - 10635 - 106
77chain 'H' and (resid 107 through 142 )HC107 - 142107 - 142
88chain 'H' and (resid 143 through 221 )HC143 - 221143 - 221
99chain 'L' and (resid 1 through 25 )LD1 - 251 - 25
1010chain 'L' and (resid 26 through 89 )LD26 - 8926 - 89
1111chain 'L' and (resid 90 through 112 )LD90 - 11290 - 112
1212chain 'L' and (resid 113 through 127 )LD113 - 127113 - 127
1313chain 'L' and (resid 128 through 146 )LD128 - 146128 - 146
1414chain 'L' and (resid 147 through 162 )LD147 - 162147 - 162
1515chain 'L' and (resid 163 through 173 )LD163 - 173163 - 173
1616chain 'L' and (resid 174 through 210 )LD174 - 210174 - 210
1717chain 'C' and (resid 1 through 103 )CE1 - 1031 - 75
1818chain 'C' and (resid 104 through 278 )CE104 - 27876 - 237
1919chain 'C' and (resid 279 through 388 )CE279 - 388238 - 344
2020chain 'A' and (resid 1 through 17 )AG1 - 171 - 17
2121chain 'A' and (resid 18 through 73 )AG18 - 7318 - 73
2222chain 'A' and (resid 74 through 91 )AG74 - 9174 - 91
2323chain 'A' and (resid 92 through 142 )AG92 - 14292 - 142
2424chain 'A' and (resid 143 through 152 )AG143 - 152143 - 152
2525chain 'A' and (resid 153 through 164 )AG153 - 164153 - 164
2626chain 'A' and (resid 165 through 181 )AG165 - 181165 - 181
2727chain 'A' and (resid 182 through 206 )AG182 - 206182 - 206
2828chain 'A' and (resid 207 through 221 )AG207 - 221207 - 221
2929chain 'B' and (resid 1 through 25 )BH1 - 251 - 25
3030chain 'B' and (resid 26 through 47 )BH26 - 4726 - 47
3131chain 'B' and (resid 48 through 74 )BH48 - 7448 - 74
3232chain 'B' and (resid 75 through 112 )BH75 - 11275 - 112
3333chain 'B' and (resid 113 through 127 )BH113 - 127113 - 127
3434chain 'B' and (resid 128 through 149 )BH128 - 149128 - 149
3535chain 'B' and (resid 150 through 162 )BH150 - 162150 - 162
3636chain 'B' and (resid 163 through 173 )BH163 - 173163 - 173
3737chain 'B' and (resid 174 through 184 )BH174 - 184174 - 184
3838chain 'B' and (resid 185 through 196 )BH185 - 196185 - 196
3939chain 'B' and (resid 197 through 210 )BH197 - 210197 - 210

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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://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