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- PDB-8wte: Crystal structure of TCR in complex with HLA-A*11:01 bound to KRA... -

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基本情報

登録情報
データベース: PDB / ID: 8wte
タイトルCrystal structure of TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide (VVGAVGVGK)
要素
  • (T-cell receptor ...T細胞受容体) x 2
  • Beta-2-microglobulinΒ2-ミクログロブリン
  • KRAS-G12V nonamer peptide
  • MHC class I antigen (Fragment)
キーワードIMMUNE SYSTEM (免疫系) / T cell receptor (T細胞受容体) / KRAS-G12V / HLA-A*11:01
機能・相同性
機能・相同性情報


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / 小胞体 / ゴルジ体 / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / ゴルジ体 / 小胞体 / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / 生体膜 / identical protein binding / 細胞膜 / 細胞質基質
類似検索 - 分子機能
Β2-ミクログロブリン / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / 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
Β2-ミクログロブリン
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.17 Å
データ登録者Zhang, M.Y. / Luo, L.J. / Xu, W. / Guan, F.H. / Wang, X.Y. / Zhu, P. / Zhang, J.H. / Zhou, X.Y. / Wang, F. / Ye, S.
資金援助 中国, 6件
組織認可番号国
Ministry of Science and Technology (MoST, China)2021YFC2300503 中国
Ministry of Science and Technology (MoST, China)2021YFC2502300 中国
Ministry of Science and Technology (MoST, China)2022YFC2304705 中国
Ministry of Science and Technology (MoST, China)2022YFA0912400 中国
Ministry of Science and Technology (MoST, China)2020YFA0908500 中国
National Natural Science Foundation of China (NSFC)31971127 中国
引用ジャーナル: Commun Biol / 年: 2024
タイトル: Identification and affinity enhancement of T-cell receptor targeting a KRAS G12V cancer neoantigen.
著者: Zhang, M. / Xu, W. / Luo, L. / Guan, F. / Wang, X. / Zhu, P. / Zhang, J. / Zhou, X. / Wang, F. / Ye, S.
履歴
登録2023年10月18日登録サイト: PDBJ / 処理サイト: PDBC
改定 1.02024年5月1日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Database references / カテゴリ: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name

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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: T-cell receptor alpha chain
B: T-cell receptor beta chain
H: MHC class I antigen (Fragment)
I: Beta-2-microglobulin
J: KRAS-G12V nonamer peptide
C: T-cell receptor alpha chain
D: T-cell receptor beta chain
E: MHC class I antigen (Fragment)
F: Beta-2-microglobulin
G: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)187,61110
ポリマ－187,61110
非ポリマー00
水9,098505
1
A: T-cell receptor alpha chain
B: T-cell receptor beta chain
H: MHC class I antigen (Fragment)
I: Beta-2-microglobulin
J: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)93,8065
ポリマ－93,8065
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: T-cell receptor alpha chain
D: T-cell receptor beta chain
E: MHC class I antigen (Fragment)
F: Beta-2-microglobulin
G: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)93,8065
ポリマ－93,8065
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)45.600, 96.142, 117.789
Angle α, β, γ (deg.)80.826, 82.145, 78.590
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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T-cell receptor ... , 2種, 4分子 ACBD

#1: タンパク質 T-cell receptor alpha chain


分子量: 22105.652 Da / 分子数: 2 / 変異: T159C / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Trav7-2, TRAV7D-2, Trav7d-2 / 発現宿主: Escherichia coli (大腸菌)
#2: タンパク質 T-cell receptor beta chain


分子量: 27310.738 Da / 分子数: 2 / 変異: S170C / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Trbv2 / 発現宿主: Escherichia coli (大腸菌)

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タンパク質 , 2種, 4分子 HEIF

#3: タンパク質 MHC class I antigen (Fragment)


分子量: 31855.051 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: HLA-A / 発現宿主: Escherichia coli (大腸菌)
#4: タンパク質 Beta-2-microglobulin / Β2-ミクログロブリン


分子量: 11748.160 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: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769

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タンパク質・ペプチド / 非ポリマー , 2種, 507分子 JG

#5: タンパク質・ペプチド KRAS-G12V nonamer peptide


分子量: 785.951 Da / 分子数: 2 / 変異: S170C / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 505 / 由来タイプ: 天然 / 式: H2O

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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: 2.55 Å3/Da / 溶媒含有率: 51.81 %
結晶化温度: 289.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 / 詳細: 20% (w/v) PEG 3350 0.2 M sodium citrate.

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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: SSRF / ビームライン: BL02U1 / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER2 S 9M / 検出器: PIXEL / 日付: 2022年8月28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: 0.97918 Å / 相対比: 1
反射解像度: 2.17→115.59 Å / Num. obs: 98037 / % possible obs: 96 % / 冗長度: 2.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.052 / Rrim(I) all: 0.089 / Net I/σ(I): 5.3
反射 シェル解像度: 2.17→2.29 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12909 / CC1/2: 0.857 / Rpim(I) all: 0.26 / Rrim(I) all: 0.446 / % possible all: 86.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
HKL-2000データ削減
HKL-2000データスケーリング
Coot1.17.1_3660モデル構築
PHENIX1.17.1_3660位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.17→39.01 Å / SU ML: 0.2505 / 交差検証法: FREE R-VALUE / 位相誤差: 23.7453
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2157 4770 -
Rwork0.1712 93232 -
obs-97700 96 %
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: 52.87 Å2
精密化ステップサイクル: LAST / 解像度: 2.17→39.01 Å
タンパク質核酸リガンド溶媒全体
原子数12926 0 0 505 13431
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005313258
X-RAY DIFFRACTIONf_angle_d0.716717958
X-RAY DIFFRACTIONf_chiral_restr0.0471870
X-RAY DIFFRACTIONf_plane_restr0.0042344
X-RAY DIFFRACTIONf_dihedral_angle_d16.79484888
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.190.31131450.23223121X-RAY DIFFRACTION97.26
2.19-2.220.26221590.22673134X-RAY DIFFRACTION97.4
2.22-2.240.28111320.22042665X-RAY DIFFRACTION83.72
2.25-2.270.27491140.22422170X-RAY DIFFRACTION93.64
2.27-2.30.29081560.21013099X-RAY DIFFRACTION97.78
2.3-2.340.28991660.20643113X-RAY DIFFRACTION97.47
2.34-2.370.27181840.20183171X-RAY DIFFRACTION97.67
2.37-2.40.23491980.20253179X-RAY DIFFRACTION97.83
2.4-2.440.25591830.19193091X-RAY DIFFRACTION97.7
2.44-2.480.23621850.19043128X-RAY DIFFRACTION97.56
2.48-2.520.24691700.19513218X-RAY DIFFRACTION97.69
2.52-2.570.23741710.18493135X-RAY DIFFRACTION98.01
2.57-2.620.22921350.18423151X-RAY DIFFRACTION97.74
2.62-2.670.28111490.19353253X-RAY DIFFRACTION97.59
2.67-2.730.28391480.18883135X-RAY DIFFRACTION97.74
2.73-2.790.24361610.19283169X-RAY DIFFRACTION97.94
2.79-2.860.25111590.19123223X-RAY DIFFRACTION97.97
2.86-2.940.24451500.18833119X-RAY DIFFRACTION97.96
2.94-3.030.24671700.18933219X-RAY DIFFRACTION98.2
3.03-3.130.26671630.19243102X-RAY DIFFRACTION97.67
3.13-3.240.21171720.17933185X-RAY DIFFRACTION97.19
3.24-3.370.23571510.17723164X-RAY DIFFRACTION97.87
3.37-3.520.22031430.17393204X-RAY DIFFRACTION97.72
3.52-3.710.18831420.15663135X-RAY DIFFRACTION97.24
3.71-3.940.18111670.15673156X-RAY DIFFRACTION97.88
3.94-4.240.17371680.14223181X-RAY DIFFRACTION97.78
4.24-4.670.17021590.1323162X-RAY DIFFRACTION97.59
4.67-5.340.18131320.13633178X-RAY DIFFRACTION97.35
5.34-6.720.20121520.17713172X-RAY DIFFRACTION97.59
6.72-39.010.18481860.16143100X-RAY DIFFRACTION96.45
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)
11.29051971271.123611016810.06678961267544.600147373820.8777724915994.203593397320.002681767607870.03626545854970.0207285128999-0.126020749264-0.0644119629627-0.0462599736126-0.3176259043750.1379053047580.007039379905220.2333045371840.0270938789041-0.004333242425250.2083480751990.01273020692570.26372355262.38979790015-22.6313969651-45.0330719181
27.846655297241.16588814992-4.803368938223.75869213155-0.02801616608346.795442541780.0191041414840.1480230921370.105119521311-0.292494274631-0.04028232964220.401125951006-0.257681033857-0.2439684944480.02917212788380.3731516339420.0633552718671-0.03509672264650.243848226930.03141992228730.306832070902-2.62094757282-19.0959008436-51.5325426342
31.32579279384-0.487457356324-0.1598654471183.57468827192.47840100414.56960817033-0.0428284242337-0.1515402336090.1689600576780.2682769006790.03811159600240.320758897881-0.369946812062-0.226834892474-0.02874267830930.3409326132510.01250822404270.05226176906750.2018654237760.0599060804830.257243887193-1.41928227925-20.3100623047-38.2073245603
46.992104240242.6479450109-2.252208991586.78200199123-1.636869429735.714982832770.0520747836715-0.08256097860850.2187328343530.979772167434-0.1122672700370.0650233958836-0.6858772643240.1698679757460.1086363653211.008851735210.01621150315330.08464245985180.433339139513-0.02877397999370.463974015416-3.11251205624-13.4432555769-10.1569454222
56.52868005619-4.7410630314.513039439524.47574076448-4.321370452495.605038825960.635705655542-0.01304729408410.5522354446580.373391793193-0.438071343506-0.7226744265260.1111845002491.24412961226-0.2144126188851.18118928254-0.117127550146-0.02762360472750.616266526732-0.02754623088260.8744695672219.22807827756-14.9950114816-13.0185137495
65.418474260842.518191726210.200029225165.14311617614-1.351712649482.927050990410.2760798572380.1726761475280.461031226320.903733972603-0.1068834359820.7097681722130.1461004800040.0771534114951-0.04440522908430.9982185142970.03857610929420.1324736637470.396641710401-0.04327166978730.686293893304-2.14050420095-11.399023064-15.3141938152
71.979701583980.1184693333590.6220409492931.50745142860.1530792572336.45716068584-0.000190124841923-0.14039540434-0.07743246106160.184918603709-0.06191759969930.01754726251690.223334465913-0.004540597312140.0687627990990.3314423384140.04835152879480.007532436114390.2168165365960.03215081357620.2831247344327.29668621745-41.6339914929-35.4062564464
82.04539035913-0.6595954407371.601063120611.82446072331-0.05262959237087.03155210555-0.02403741328440.0925963358387-0.2477841421580.155105475333-0.0129841567916-0.1578189486620.604555711750.405581942850.04049414995350.3145981333580.01110743314580.02322191272090.2367462985420.02496531020110.3704463307389.27522786552-43.2943434611-40.2585375604
92.7003068874-2.34687800754-1.368235936765.206340050711.473570996362.36617714649-0.171632200399-0.3464277807570.108612264631.095166651930.1326351280970.1968260106560.05727500426260.0312459369116-0.02699843658960.825891474466-0.06196778851430.06005024051390.4618195560440.04022474667770.3231784021470.997878658891-27.4951389934-11.6885194247
105.94203359868-2.065817435160.1052736177173.42386436408-0.5962257733111.040115256240.00285036476807-0.245109216459-0.08821040907790.4130904083780.1377870972630.3334807061240.0653879671719-0.186901043037-0.1073654052440.797433918275-0.06262281336720.09666031249670.5021030314660.01859151756590.383046147461-4.21226654571-30.2925493522-12.7204212969
111.96320953647-0.302190076092-0.451273274411.783083174170.2341990642341.55656502471-0.0909701313889-0.01082666566470.0249780029302-0.06303744932050.08095574275580.031642969695-0.03310034408040.07646238230930.001800235247910.2207739357960.0100370793482-0.03168224056730.237926563128-0.01262328368460.2410358217284.64884071667-45.0367762331-66.9839123707
122.09754842243-0.003374246997010.8869838914132.912991589752.047795124216.32406416406-0.02970361770340.5597259790020.137669761603-0.9004062259840.1445761389620.327606711299-0.4650247295690.0738388142462-0.05641483628760.594407183695-0.0313337359075-0.03756834517360.4727742699120.07330173284570.36582599485110.4775126604-49.8272790087-101.213131612
136.107157595570.43885290392-5.125538623432.87943168395-0.339547402794.36457642712-0.4163556805530.4770155246520.0509247615182-0.3575485961720.06868497727370.362993187556-0.119979970921-0.7557531455290.2773348761710.3847275217450.0409430696033-0.0795187927770.454548410984-0.05857284484780.3446112017522.91129579313-60.9103374108-85.4710820522
147.90246400009-1.9490719537-1.075687051698.131255774451.655556418370.4029057906990.7298970670490.2062747386740.798819850572-1.2193003914-0.181097103513-1.5019319562-0.0860121012661.0943596021-0.5651838017420.5349716137640.02841798019010.1529908045540.594185363372-0.008849536106110.44224538310925.1714570735-61.2021746219-93.4794511893
157.46165436298-4.34420917023-5.377468808313.570707064512.807353566714.27084953595-0.182406663761-0.2546857270860.0253843446127-0.08666358075460.119589179318-0.1699126798460.2441983897110.1955819177560.02568740818360.3740482719730.00187597279882-0.05079869737730.322168717421-0.03000372448330.31971714105512.9986833604-60.7381846524-85.0849396024
166.73435021559-5.99847541756-7.586728864495.447083105816.971110850459.80208639488-0.985912833917-0.586699602443-1.190584751130.8405223918440.2190757102181.054943516751.095969671820.4316545251450.7767654306360.4922108824570.01628749481890.08851758993530.3544488941660.03236883039240.5052760177359.98744780087-69.9359273134-80.475737954
178.21884490871-5.72943186489-0.9234785090584.330964557370.2489238945230.5642136022810.0134033435095-0.954025871409-0.9231429349641.326243284910.173864154378-0.9908733615310.5528812516910.69140325449-0.09361483829080.6646291487550.265849569419-0.1439236596030.5156885264240.09137682527580.57177357371218.2507628882-66.5624953034-76.5924433041
184.2274123802-4.78420063836-5.165813439386.195027810785.596430812276.348555444540.3038835421880.2024492266860.704260087788-0.235639172948-0.0411478159049-0.442610395427-0.1469039367280.378187353949-0.1701819068450.3147981298160.01080552369240.0033717169810.3484224363070.07007236748650.2791517475469.24695852568-56.9786506431-79.6173583908
199.275281398652.67582322244-4.96710817446.596253785-1.806081798312.68375325089-0.4190023883051.12077774184-0.686411318137-0.919532466032-0.0505683997305-0.7852199192871.021163198130.2446945213160.5399090162830.6567172146810.1767980149460.01642115271540.729160320834-0.1133961368080.53954365030822.6895721419-73.231006026-94.9190918268
202.4615933114-3.54405872935-3.913018676925.138238986095.600596533266.25004994791-0.1661655195740.808627252385-1.028046168350.200015502926-0.6163676164940.7295216345030.347828061829-0.8429559773540.7851088060730.410113649039-0.0316635465168-0.02151244847360.345225678764-0.03820649847460.4577763293043.62879935515-70.6373454288-83.3537186048
217.83646840958-1.174786946131.629375512778.36244126712-2.032454090394.439573071910.6256355250381.727602364010.00646624575719-1.04576353928-0.3251110594460.7188239810490.4367772692950.0523634380392-0.0461780721420.587962335032-0.02332262264-0.01003667307660.537263377857-0.1434195436410.33900004594412.1633345291-67.3858369076-94.6823643367
222.08286457251-1.14852218288-2.732599389981.480277706890.4210857203615.0621470930.17544819130.0449029243519-0.844525367117-0.0557258644797-0.3587267007980.182894197239-0.3472641257230.2952962008760.2510563684020.2319717655890.0237967114283-0.05830386397680.277507757265-0.03695885163930.4245337729442.32932608632-42.5553625289-61.4740165874
234.151649901420.1300359430952.197252398244.613890137851.977635690652.86204152595-0.262470082645-0.1354967686490.2923799564130.289545481633-0.05638648219660.1421081693750.2600818480240.1430447478450.2162626747570.4447554144850.012373368608-0.005161448266650.2119382635720.01960747207820.340793401317-11.4592901411-103.03542909-51.087062193
244.58659221990.0824010475313-4.002852703523.937024824861.367398400177.160586839230.180524121487-0.03529646676970.2632263512540.2296985064480.04489879930410.0544806965962-0.199756825561-0.178131295737-0.238754862080.335984745894-0.00931310695965-0.06776945817410.1487169911950.01183076494330.329509176647-12.6067884235-91.1397739998-46.8804003789
255.094770559062.074362967563.521063510942.792343627871.324786551262.75439450363-0.0427694465101-0.08735485739640.2077247139470.402560306378-0.2276235019740.574875066160.0708207441139-0.1523748427030.3049715060250.4420912636790.05015363806850.02249179486080.2253390420450.001830103585880.352742481984-20.5007439094-97.7456803095-45.6121707227
262.003044304422.335397271771.245461212123.984718493573.387354779185.202370619820.0174954571084-0.1628514879880.1459185078680.0364778173933-0.1333859989620.2959616277880.156626497494-0.2933367692380.008103532541580.3533326808460.0521889248327-0.04337295778510.1955846118140.02809595394140.301148448474-11.5179501382-92.9888273485-49.7931157471
273.309669941850.205296397679-0.1647330860264.863503949434.728428525254.66153751232-0.3729589261570.451650583462-0.0119059438393-1.04831009447-0.07740656819230.505550390649-0.960608294815-0.9579224125910.3466256607450.685488065186-0.0497996092901-0.03706645562410.433856776029-0.001032816001290.38039900633-16.0772405038-106.239243067-70.2247146113
283.501757799250.419656070110.1959095242044.62638207482-0.5871965628734.69627723367-0.4395706373240.277439137429-0.172910547543-0.6113797108220.374019639042-0.188975980650.01734786607490.009417699411780.1685263811040.85565119621-0.1695883939730.08663701267430.445253270201-0.04924770432430.502302507607-2.50199241568-105.866537247-82.9081798361
298.71359786085-2.85200351456-3.121132532758.09464214068-1.58444943327.75484388772-0.51688408911-0.450982770012-0.222886930552-0.2688685685020.2474486664750.1004783713890.3451477003940.2962407486790.2636093798670.704849352998-0.08916000669690.01542965514380.379583420420.0109323710540.404768539896-3.13651295121-104.251196202-75.9979518502
306.22492896126-2.257061099471.513823856483.915707556920.8664085976766.80958139307-0.2650754331890.559778964263-0.465016875885-1.115855264880.5583087302560.4997485586790.613060376436-0.798292849097-0.4529645829310.943535009048-0.1320284053950.1737992248620.502583736466-0.1409280157860.8018914371440.211464231628-115.209198331-79.2624327488
315.28891632633-2.135506418-3.074376540683.453368731331.415370897484.785102569480.2429355288280.184543097220.484490602237-0.09709367891490.0358798496594-0.321171408632-0.01376031166180.301923923853-0.2346295824760.251985572933-0.0458152729963-0.06120758755840.258948447602-0.01490647131490.2985145511751.59104778681-77.7753489854-55.5599504156
322.882423862361.72704723153-0.00887077322.270927907911.588420619222.425949087210.006469193029420.0100841492999-0.03791517514270.5108317469240.186440308086-0.9315071336881.001317851440.530788552698-0.3918139733650.4582554310410.0688464744001-0.06555173830760.424672059162-0.006505892266550.3289322981911.54104330276-86.6643543692-47.7118828001
333.84703569120.480887401775-2.258858596031.794776889761.066309584315.015994003710.050177677042-0.2902817052270.1790098161880.2426385912370.153313664151-0.176534359728-0.135613188830.586680781086-0.1925714704930.3590457909730.019373989639-0.04309018105780.268287139860.01497669090740.312763453921.24122449848-78.7296377766-48.0228916815
345.12785986762-0.3650215806670.2752459222036.860600319092.700993586046.74903301221-0.6450494545430.04267835209060.01108132973830.03219983103810.506568277781-0.6726087951430.6967049524511.013755683660.1563807296390.3196230229280.076656914003-0.01135745986030.452512786218-0.01276107582850.39826030233714.8762953686-87.3376588392-66.4477423441
355.70788432265.748791525366.251381495128.040827069024.086493003159.47885666203-0.6157736304360.854612062011-0.397478816764-0.9680003314650.5186232171270.1423641803390.2799229699690.03815101771310.1798934964650.825336468159-0.1550446736810.01548625274980.487210708577-0.02379755724880.480437959753-5.55464350777-100.120968262-89.5334826463
363.723145434382.56193730663.775592049313.19242909010.9407752488796.80899844225-0.1981432386790.0960823600791-0.204088246847-0.3259674196390.2640426636420.02170857364960.183899190872-0.17861698938-0.06193936925710.548053569942-0.0524132170950.04957281833490.3633406587810.004145386352720.339565330898-1.42182305508-93.19090889-78.0617263177
376.748030613490.3962516668445.681953673721.154356664910.870069413768.06986244951-0.6976251193770.6581592970990.810264754168-0.6131368050140.260959866958-0.0485485761433-0.03098018156030.3891656721690.4372308265310.720836943091-0.1565932530240.01028164499870.4811134444890.1643471873110.4423358457895.21051247505-83.9903959988-82.1008257555
381.39438995949-0.161820004418-0.4367591219012.132267822560.7352242073262.656213362650.0604744758379-0.0116328490607-0.03046231869620.246663891541-0.03752923689680.05501604261930.0460815018880.0925694356025-0.02435690346480.411503551501-0.005876744661520.02416845999610.240510010011-0.05374883739780.290881732069-13.9777835143-73.5571645379-26.9823767316
395.68196481348-1.39677424063-2.634975539473.246015691111.797837166885.988532096860.0655318523564-0.06552763289830.1399020396120.1804504106790.03264119457760.1952524754370.836958217867-0.438504792801-0.06596134938850.660340992688-0.0955386198677-0.02410007074010.4307788089140.04947178193340.295520720758-23.2868720392-67.92952316636.05367307093
404.97842230728-4.442571090244.7221036975.7763802116-4.277304187424.60010913589-0.00588833938657-0.3970463895980.1807446645490.1360987609550.07271651079570.257437687487-0.918027747012-0.289481019602-0.07994158234180.6360810779850.004926549197220.1022792793370.435293279183-0.04420350152050.353858136629-18.6433350716-56.736350923-10.0458577703
414.970165986074.860828123352.399258277534.767386078342.36623303021.18431603810.559619444105-0.708277922022-0.7399557599490.781341992789-0.192473779915-0.9012462712861.369687238611.10839704807-0.3654042679540.8179437400090.200535835135-0.06714989441780.785256384066-0.08004419211190.453599039913-3.44180925676-62.92247367177.11951860755
422.048604073770.3935591909431.935343480421.470923033721.244870212244.359663096970.04848533765890.4086492536740.155501058632-0.4716217165430.102833808702-0.254666214314-0.7937768582321.95415323123-0.1042508635950.752291260213-0.1177479222630.1682632005790.724226753212-0.05559923127780.351262870522-10.138721765-56.3722615255-9.83612811776
430.999973507202-0.0357177678121.75878290173.349103308151.379674640494.475290028980.114217489765-0.137741428357-0.04072127268250.0288941853520.00431448767523-0.324113377463-0.2357614115491.48392581493-0.1211625221050.595140827998-0.1678419089240.1458566773340.843474429664-0.007210255946040.313899771858-9.26705448018-58.9217412544-13.1011973687
441.96680631221.645587197834.052254588051.868294982723.247634629648.495923507760.06782189706330.09534753902340.3537225520360.1052112506120.193643215088-0.133120114135-0.009167908071582.01787616934-0.05264351250190.59554029328-0.1813792093930.1165001946890.882944688384-0.1268898302220.391834660309-5.31987578471-56.9649199764-2.55547106568
459.25754133367-1.916339760821.975790874711.53710552392-2.305637052573.5845574320.7063123101440.2400553613530.506153344358-0.796872064397-0.0317668221029-0.01169798219560.6303984981841.58941122836-0.5498374151231.03397781157-0.2805886282920.08685415382660.671016545242-0.02363476371940.430692020124-9.43999001154-49.6965339803-6.58948116442
468.16343647548-0.02634739439650.4845957252026.420505082572.307931265180.8596771398490.640532247116-0.3456241956550.994805466888-0.662804555045-0.9185327913160.667490511359-1.44293290188-0.03638869882310.3514732121691.36878133638-0.116266458868-0.05412413103990.377713217948-0.04714780105660.475310969144-18.1139181567-46.2681637423-15.0160045059
471.98923347984-1.986245316982.926858103623.20226731084-4.406833733446.12708630503-0.0653414426916-0.7387534467080.4731729113-0.091853941790.4924129724020.363182201463-0.9497954021630.340133319508-0.5088117475920.772350238087-0.02474220556710.1156643090670.602279761334-0.06783600208530.47590677286-12.8469435272-52.91098469862.81290633053
487.91970460875-5.02721190438.020584783774.2349072392-5.688129356638.46260276008-0.128276811882-0.5059503138090.681154356372-0.0439744667363-0.353003190987-0.5849113510780.646586622542-0.3464423565850.4276035152370.4614270242620.03773770448980.009577417695380.262109938479-0.08975430125520.372868416698-14.3275938364-75.757197037-33.0301366466
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 147 )
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 192 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 107 )
9X-RAY DIFFRACTION9chain 'B' and (resid 108 through 138 )
10X-RAY DIFFRACTION10chain 'B' and (resid 139 through 239 )
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 174 )
12X-RAY DIFFRACTION12chain 'H' and (resid 175 through 274 )
13X-RAY DIFFRACTION13chain 'I' and (resid 1 through 11 )
14X-RAY DIFFRACTION14chain 'I' and (resid 12 through 19 )
15X-RAY DIFFRACTION15chain 'I' and (resid 20 through 30 )
16X-RAY DIFFRACTION16chain 'I' and (resid 31 through 46 )
17X-RAY DIFFRACTION17chain 'I' and (resid 47 through 51 )
18X-RAY DIFFRACTION18chain 'I' and (resid 52 through 71 )
19X-RAY DIFFRACTION19chain 'I' and (resid 72 through 77 )
20X-RAY DIFFRACTION20chain 'I' and (resid 78 through 90 )
21X-RAY DIFFRACTION21chain 'I' and (resid 91 through 99 )
22X-RAY DIFFRACTION22chain 'J' and (resid 1 through 9 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 25 )
24X-RAY DIFFRACTION24chain 'C' and (resid 26 through 53 )
25X-RAY DIFFRACTION25chain 'C' and (resid 54 through 76 )
26X-RAY DIFFRACTION26chain 'C' and (resid 77 through 104 )
27X-RAY DIFFRACTION27chain 'C' and (resid 105 through 118 )
28X-RAY DIFFRACTION28chain 'C' and (resid 119 through 147 )
29X-RAY DIFFRACTION29chain 'C' and (resid 148 through 176 )
30X-RAY DIFFRACTION30chain 'C' and (resid 177 through 192 )
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 35 )
32X-RAY DIFFRACTION32chain 'D' and (resid 36 through 48 )
33X-RAY DIFFRACTION33chain 'D' and (resid 49 through 107 )
34X-RAY DIFFRACTION34chain 'D' and (resid 108 through 122 )
35X-RAY DIFFRACTION35chain 'D' and (resid 123 through 138 )
36X-RAY DIFFRACTION36chain 'D' and (resid 139 through 196 )
37X-RAY DIFFRACTION37chain 'D' and (resid 197 through 239 )
38X-RAY DIFFRACTION38chain 'E' and (resid 1 through 174 )
39X-RAY DIFFRACTION39chain 'E' and (resid 175 through 275 )
40X-RAY DIFFRACTION40chain 'F' and (resid 1 through 11 )
41X-RAY DIFFRACTION41chain 'F' and (resid 12 through 19 )
42X-RAY DIFFRACTION42chain 'F' and (resid 20 through 41 )
43X-RAY DIFFRACTION43chain 'F' and (resid 42 through 61 )
44X-RAY DIFFRACTION44chain 'F' and (resid 62 through 77 )
45X-RAY DIFFRACTION45chain 'F' and (resid 78 through 83 )
46X-RAY DIFFRACTION46chain 'F' and (resid 84 through 90 )
47X-RAY DIFFRACTION47chain 'F' and (resid 91 through 99 )
48X-RAY DIFFRACTION48chain 'G' and (resid 1 through 9 )

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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