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- PDB-9ek6: Crystal structure of MAIT TCR in complex with MR1-5FU -

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基本情報

登録情報
データベース: PDB / ID: 9ek6
タイトルCrystal structure of MAIT TCR in complex with MR1-5FU
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha
  • TCR beta
キーワードIMMUNE SYSTEM / receptor
機能・相同性
機能・相同性情報


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / endoplasmic reticulum membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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
ACETATE ION / THYMINE / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.22 Å
データ登録者Awad, W. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号
Australian Research Council (ARC) オーストラリア
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2025
タイトル: Mitochondria regulate MR1 protein expression and produce self-metabolites that activate MR1-restricted T cells.
著者: Prota, G. / Berloffa, G. / Awad, W. / Vacchini, A. / Chancellor, A. / Schaefer, V. / Constantin, D. / Littler, D.R. / Colombo, R. / Nosi, V. / Mori, L. / Rossjohn, J. / De Libero, G.
履歴
登録2024年12月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年5月7日Provider: repository / タイプ: Initial release
改定 1.12025年5月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: TCR alpha
E: TCR beta
F: Beta-2-microglobulin
G: TCR alpha
H: TCR beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)189,11920
ポリマ-188,1008
非ポリマー1,01912
22,7531263
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR alpha
H: TCR beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,55210
ポリマ-94,0504
非ポリマー5026
724
タイプ名称対称操作
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: TCR alpha
E: TCR beta
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,56810
ポリマ-94,0504
非ポリマー5176
724
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)216.366, 70.042, 142.518
Angle α, β, γ (deg.)90.000, 104.250, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

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タンパク質 , 4種, 8分子 ACBFDGEH

#1: タンパク質 Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


分子量: 31711.670 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: MR1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q95460
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 2 / Fragment: UNP residues 21-119 / 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
#3: タンパク質 TCR alpha


分子量: 22781.268 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#4: タンパク質 TCR beta


分子量: 27677.760 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)

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非ポリマー , 6種, 1275分子

#5: 化合物 ChemComp-TDR / THYMINE / チミン


分子量: 126.113 Da / 分子数: 2 / 由来タイプ: 合成 / : C5H6N2O2 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 7 / 由来タイプ: 合成 / : C3H8O3
#7: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 1 / 由来タイプ: 合成 / : C2H3O2
#8: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / : Na
#9: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 1 / 由来タイプ: 合成 / : Ca
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1263 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 2.78 Å3/Da / 溶媒含有率: 55.79 %
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: PEG3350, sodium acetate, BTP

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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: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: AGILENT ATLAS CCD / 検出器: CCD / 日付: 2018年5月3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: 0.9537 Å / 相対比: 1
反射解像度: 2.22→46.04 Å / Num. obs: 102344 / % possible obs: 99.71 % / 冗長度: 3.8 % / Biso Wilson estimate: 37.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.71
反射 シェル解像度: 2.22→2.29 Å / 冗長度: 3.8 % / Num. unique obs: 10158 / CC1/2: 0.756

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimless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 / 解像度: 2.22→46.04 Å / SU ML: 0.2525 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.2266
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2099 5222 5.11 %
Rwork0.1814 97064 -
obs0.1829 102286 99.73 %
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: 44.95 Å2
精密化ステップサイクル: LAST / 解像度: 2.22→46.04 Å
タンパク質核酸リガンド溶媒全体
原子数12732 0 66 1263 14061
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.001713438
X-RAY DIFFRACTIONf_angle_d0.504718336
X-RAY DIFFRACTIONf_chiral_restr0.04081950
X-RAY DIFFRACTIONf_plane_restr0.00362395
X-RAY DIFFRACTIONf_dihedral_angle_d20.73184879
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.250.29471860.26753189X-RAY DIFFRACTION99.53
2.25-2.270.30811750.26873264X-RAY DIFFRACTION99.65
2.27-2.30.29291520.25943180X-RAY DIFFRACTION99.64
2.3-2.330.29451700.25783258X-RAY DIFFRACTION99.88
2.33-2.360.29261730.25233176X-RAY DIFFRACTION99.85
2.36-2.390.28741760.24673209X-RAY DIFFRACTION99.79
2.39-2.430.28261610.23913262X-RAY DIFFRACTION99.8
2.43-2.460.3021690.23983189X-RAY DIFFRACTION99.58
2.46-2.50.27621850.23853247X-RAY DIFFRACTION99.74
2.5-2.540.2951550.24193187X-RAY DIFFRACTION99.94
2.54-2.590.29332170.23633229X-RAY DIFFRACTION99.88
2.59-2.630.29881800.23733171X-RAY DIFFRACTION99.88
2.63-2.680.26351630.23373247X-RAY DIFFRACTION99.8
2.68-2.740.25571760.23773229X-RAY DIFFRACTION99.94
2.74-2.80.2851660.24523238X-RAY DIFFRACTION99.88
2.8-2.860.29941760.22663205X-RAY DIFFRACTION99.82
2.86-2.930.24251800.21033245X-RAY DIFFRACTION99.8
2.93-3.010.22031780.19353216X-RAY DIFFRACTION99.82
3.01-3.10.22381670.19413220X-RAY DIFFRACTION99.88
3.1-3.20.21091720.1823263X-RAY DIFFRACTION99.97
3.2-3.320.21491750.17943238X-RAY DIFFRACTION99.85
3.32-3.450.20861620.16893241X-RAY DIFFRACTION99.62
3.45-3.610.19211810.15963208X-RAY DIFFRACTION99.56
3.61-3.80.16381720.1533267X-RAY DIFFRACTION99.59
3.8-4.030.19081640.15173239X-RAY DIFFRACTION99.56
4.03-4.340.15591960.13153248X-RAY DIFFRACTION99.74
4.34-4.780.13461760.12083246X-RAY DIFFRACTION99.59
4.78-5.470.15351550.13693304X-RAY DIFFRACTION99.63
5.47-6.890.17321730.17143297X-RAY DIFFRACTION99.77
6.89-46.040.18881910.18133352X-RAY DIFFRACTION98.91
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.43699111928-0.104209971670.05629811855261.356471129210.8341010581411.62338123505-0.01763695266090.09378687913690.198510456249-0.1451479075590.110600125039-0.143829572462-0.01000136025810.199193951309-0.08497007461720.178088628675-0.0344180257523-0.001167191097820.2824789450350.00335461142530.2818131860250.813252444877.2010603748223.23395223
21.112923395630.155434308529-0.4144689125232.05422513288-0.06545043024970.5744533652670.004651631299-0.06236739528480.2812617264160.02904958850.04862191106660.236151820009-0.036623878586-0.0566601594618-0.0313197454880.216577828765-0.00499196081446-0.01358254835050.244585230577-0.01436005559960.32508173057838.435512870580.9054515102233.89079485
31.55757519558-0.4804112476990.5200099609850.7216035946380.180996906231.434739969620.07337183332350.0452642520072-0.1195720790880.1880499572220.210979946698-0.3299270444370.1611820329070.427811321515-0.2481068423330.2439433216390.0305328854493-0.05004190187870.320788432629-0.06629945968920.30906981011463.359964696170.2291079045242.327086004
41.225213688380.3107410409110.4694789504711.11895904586-0.4451495142771.28965203132-0.06973999207-0.2675167801350.3955893619380.336113761548-0.04183381382780.0474061617485-0.426315052824-0.200501934390.09816308772610.4393954598690.11962409539-0.07338992078520.555328953242-0.1846342728910.51619193059267.807730931979.5079595995255.815363475
52.99775647645-0.4355594956750.2504045074571.61080856561-0.2108009887671.533131143710.01046071459110.05689108653620.3114370803390.323579913407-0.05854659770630.188475628415-0.2588308509240.0635871297531-0.01599239302470.3754439580160.0181490918625-0.02874881220960.32250987224-0.1166499892880.63023527825661.91589807492.5251257026237.282492719
62.962644342531.46000693391-0.3777139098751.277829816160.4490441886590.735123203731-0.489155097512-0.442690640289-0.0266332678820.263026375535-0.271302913263-0.708246556566-0.1089946244230.9601145461610.5785484108190.4085862395130.0748084312515-0.1975501918980.99116069921-0.04249399205640.85842598011983.389162064879.5812788681240.525333649
70.6160969021560.5622986311030.4377192949210.8929350521940.2187777498160.8690303481850.2309373514960.0161674124998-0.108340052195-0.03222925329790.278744492428-0.756967214299-0.298837285930.429246373673-0.2837852902050.148116964821-0.0756052030233-0.08030709080130.564520908994-0.1141381690060.76679163132270.550480603285.1661568718235.138040524
86.16812481702-0.1943855726140.5061334125190.3464737309790.2534323217160.3559071677510.003613495797710.6628493528320.426206951035-0.173275812363-0.246426521642-0.187962182084-0.3314281495480.5298929686660.1625343851460.323750489493-0.118223779662-0.009148977165190.5660715995850.1610647858170.6415272745266.468174151792.9352469335228.54508113
92.36052506151.1523892499-0.4049726383562.88471492409-0.3251033524151.22860339462-0.004600309696820.3830933180410.399601767896-0.683613595895-0.343867990485-0.284130990436-0.1138041160730.2521718262650.2083734660350.37431423239-0.07658469505070.01890291896990.8216704708140.01138088991290.79817856272276.73501869289.2134215171226.160535923
106.99149214203-1.13558813947-2.39154710752.478353520050.8047622917993.272525201410.116896050123-0.1326543521810.06595050254530.2291767192940.119740848464-0.3034665655430.2611458402130.529468046106-0.2055781017510.274411085827-0.00597359897443-0.05422359407280.307268701886-0.01461590429360.39889728192255.261264697683.7175419097232.830865631
114.351862485920.355867223551-0.09903878306070.774726242789-0.05203671580931.01594691373-0.3547154079360.558696189220.322533633516-0.1071613583510.217237786431-0.4546072507150.007602779986960.4498332947930.07096493392130.266666840306-0.0384853952178-0.006190416747590.549831571494-0.0286050076150.55110732137971.13313624383.9314000684231.457792157
12-0.00201791464876-0.003927979613550.001768655561910.0041397534219-0.00679213957106-0.01136326760520.1978798752950.02517313044750.1752114880210.1233771679610.231481624214-0.2823676031520.01818854254640.080185182465-0.1810840845190.301801498899-0.00377503005924-0.2644797434171.34645929505-0.07841080720351.4587126241987.811749420190.0960626271237.677089401
132.486516099920.977749339469-0.9622380096431.110140667370.556881786711.529383597020.322683864670.1222766435070.132076997379-0.0127368317366-0.0789348175842-0.800685437349-0.2181309471760.281526383497-0.220042456980.406374614571-0.0900063080463-0.0434697796420.5927256120340.05927786351761.0757506826573.147262080794.6394659208231.981970745
142.644861151120.2939665056060.2804548849591.024742786980.3405580155731.21591819559-0.1498582047830.1185696896850.4750324307010.2430629581840.289110537536-0.192392642298-0.3326945011480.518838199483-0.1597258606230.403514666263-0.0563735728049-0.08467033038290.564423407895-0.09375828566870.87282396144369.919362501997.0605420402235.926771853
150.968921897188-0.144636813977-0.2362146209651.4405432551-0.6356576569591.809532343080.0780591694220.1358195910320.00154138838532-0.0282549695653-0.1000206425620.204687741235-0.08644701940340.04773724803970.02682964584810.2825205038770.007540310804510.01695281485960.299795064166-0.03982897359530.298832658737-4.0280630873163.0171797592159.790419863
161.38816988951-0.488643252236-0.09978164120351.61170209688-1.376904386270.9977131513330.0527457999317-0.0149113653325-0.05699332580850.170333520644-0.148715500528-0.0178153397629-0.03316979328340.1046995786650.08875561254050.245889767157-0.0463001268363-0.002675648601320.299483605182-0.03311161482110.2025042454193.9313439656756.2681659083170.067042185
171.605018195680.2378471131880.2042467361111.160152452930.5214248481760.845846170992-0.0455186596648-0.149160543557-0.2160045548160.0121242134278-0.05467430131310.02404161723870.0164511041479-0.1014734884770.095832772680.2985451281730.02122631229050.03973772901640.187698543498-0.01885045216930.315076392234-19.520042453772.4317753243190.436356906
183.16875009295-0.4290504051920.2050881502451.63611331010.1979349681691.91899496601-0.1696101089830.0163745624762-0.08594945145880.04083286579530.105064855930.203648303872-0.2772809912130.225461563152-0.03361028589310.302626023924-0.0346834283937-0.006797022131090.4283084348290.09238512396060.30183310668635.650476556467.1545245535156.332768921
191.65614603130.130010907553-0.4528244862960.4202538336980.4834827579371.7607971282-0.04889958449990.08946372198030.0558904457171-0.03490124924830.0455726994331-0.06938904259430.07151512868220.107794672320.0105551349940.279598300202-0.0582047835772-0.009205551765730.3399949962190.06289178298760.22138338991627.539703824161.4469779333159.370503783
201.13088338747-0.465446237713-0.5081852882090.3115181456840.131921225440.432541386927-0.0145878586159-0.229027494027-0.205722436805-0.1416958099160.0522196781641-0.2618239960610.1644519487010.635397295661-0.03410092208170.404432002660.02057258647030.009492388766290.7731959462230.0118374055910.49505540989655.025315335959.2496943654141.861786892
211.53056707806-0.5141047528870.2982636083272.10609161176-0.1820205583352.2664840213-0.0118563114075-0.1214792391170.484174375403-0.4363109050810.2273239154710.00621410760584-0.5651023386350.224536644998-0.05768852133320.677417573475-0.04343091601650.0898143464550.693313848266-0.03451912475370.65356846066954.149354542667.7513625703141.220780377
223.01750466526-0.516179644688-0.1796569857841.548383886410.1990622803472.37024656283-0.0063392499185-0.2760700393830.348937364852-0.2542192455260.343835051982-0.3584659492840.3699299573760.49388576393-0.4019114760630.602692146647-0.07369390379310.02283028451830.585416205970.0405322574070.4463198995253.45692892760.1054392774137.140323044
231.043741799431.110885454960.1918268266041.123205860860.01903855984022.82195194017-0.288479395722-0.152419585650.327959289937-0.1856428089090.24283454428-0.596286621959-0.3540079766860.6949887780950.1749144282960.750757410308-0.1552448944320.1175661700780.922036994773-0.00916284701830.68255124500763.244998043966.8334318736140.083123163
241.77903164533-0.190838547615-1.034791642041.195869317490.1822028840641.255218245210.004170798134550.4026754093390.0391848513076-0.357127458623-0.03218758050010.06791464762090.125847404305-0.3510409026890.04178648826250.406029990481-0.0779075338725-0.05084002296040.509485379480.04934822678840.23684436798715.101162006162.0040799391138.547810453
251.387226522011.054928561850.3305048258211.82246124439-1.185038412031.875822774920.273217167002-0.163401980001-0.1102483775710.0618712365319-0.3357463013440.158835117919-0.361509616027-0.4425112841140.03072471202290.410566608932-0.0838136236361-0.001338562126830.503221736332-0.002937734655880.33814388143215.90018906455.3289293446151.445170824
261.554078628410.0962700436806-1.32568874830.4638529720320.03577657859831.916190515650.2773707614480.2218201989610.546724497938-0.3399202494570.1905406875930.11761858268-0.0871142146245-0.0439599871971-0.3551861129320.614259474963-0.003736514792280.08558631419220.5797841512360.1246106613090.35278456108529.457702113266.1570843162124.220331076
270.8354748659310.5591436621560.3292605847611.595251891920.1093813676731.309790627160.197792036984-0.355846306028-0.326455244166-0.4440932022480.215701143743-0.5720806556240.1193936423160.614266653608-0.3114197023190.5574574254230.2365755880620.06997447792690.81111624083-0.06004830064440.67033420209358.812992735153.0401697115131.044383995
282.704841158870.4396940098461.147407267431.64294715732-0.1747608709832.55915162320.2738531154590.264056010144-0.383805913275-0.210173485840.0813320007174-0.01463240964710.3539390125990.288664759538-0.3155689530690.5557128410480.02710950800410.0281585568980.39702641841-0.02249223992680.3192768538242.481411143355.3742290642127.224212755
291.88011454380.5389337120440.07666864629140.795772371645-0.5490006694623.00339863012-0.2939327890150.621964095965-0.671426738499-0.417416853456-0.02958917320440.1933462051760.2981211153280.3950273912120.3324156134390.333386659147-0.0344375563774-0.02176892001340.340984728827-0.1294418949810.559944389398-18.9665734749.2379098628170.263545026
301.784575273410.132663622801-0.09132967977352.17142911310.4246529254981.72172056349-0.00310653158526-0.05989677622690.36985434510.1857265515310.0170064015830.20994581459-0.488496560465-0.3741419418380.0590916685660.3896284141090.0557716439177-0.04290698374190.279244601969-0.01549626804920.402231286552-29.245020988974.1356163663176.8483119
311.33320729392-0.177526910807-0.06076028905141.31938155040.1030984974071.28194022275-0.1708527104930.3586149542020.139336075677-0.2141786602510.05046721258730.147619894071-0.298378022032-0.01052089290540.1191483116250.305257643668-0.0174799677228-0.06686349031590.274546048086-0.01746227046240.31249679985-25.255804616365.0781800203168.109069968
325.46058814560.201894081260.5684086998561.347292897150.04753491741470.714052612767-0.2325823212590.3252821137720.363968973513-0.62367278543-0.04400933431680.425461870521-0.333577110184-0.02564859998110.1638307921930.491520328510.0294554724091-0.1386814772830.5240452144250.01436732118840.437003128269-31.503754518470.751274473161.877198681
330.524975531548-0.4824892280940.4407293904971.5607475203-0.885116856610.9492210710270.1772208683570.0002427258252810.0349423453803-0.2714429647920.161618537277-0.04470591214190.1495044150960.26537807209-0.2364163665010.375022193533-0.03570393418570.04641165584780.300474186574-0.09808704459320.309918410966-12.012431608460.4608994616168.659005701
344.46426606296-2.27873674027-0.2468293196434.138655640240.2971532757752.63802163004-0.02690246559930.318172871480.577934079039-0.6529497789070.108598610395-0.0488732456518-0.371622759156-0.2051469636790.03025635531330.414988034622-0.0460913826231-0.07521640015680.3222089402860.03292232605680.333623639045-24.203755912470.5837886883168.153554679
351.43944049109-0.152128647658-0.2203226831581.88659364770.1141482375621.099511832350.1567780547810.423822124616-0.0753898197166-0.236843911367-0.4599091252820.713208383035-0.127182852456-0.4023116714960.2906009251680.314495469015-0.0170808962312-0.08499282897180.350984902474-0.08163674132810.46892144203-33.30719483462.1224072833168.376342464
363.204415504130.117429555150.501149532495.425512951441.619470304183.84999422848-0.0645700533775-0.7313600661640.2553585369330.6727105808-0.1518387251150.919149414626-0.165873852353-0.2549882116120.1102035937630.32108102718-0.00685733853880.07327989414030.400456917079-0.0676790785250.469671250364-34.602352535966.7652475197176.727380351
371.234886529990.4951929519620.1407973858561.272431123510.3823912567051.14066183131-0.04796089210010.106839470318-0.0405790455264-0.04086387869610.1649325427590.01369014177930.1527056814360.00354223244667-0.1187124954930.275009986644-0.0295190072491-0.005591372168320.2314615912260.02937677520820.28797802977624.596352401757.2275850906220.757719886
383.939412342860.4478179873951.35246440221.225294680070.7870728674642.23981930921-0.0651101278204-0.3705193665140.158769937247-0.0405527378514-0.01404806522730.076443175453-0.136435866906-0.2057058745990.1066452992190.310725796216-0.05085181954130.0287637007910.245609791677-0.01756914029860.32519267964121.694996285958.862738229.059383087
393.033721460790.6514108761010.5440578575880.592310754106-0.06936013346890.824914394841-0.1547897473980.2033768834970.3250203989770.04295499189080.1184595449140.223614570015-0.00437219313471-0.04302539432360.03139755264780.275520863683-0.04667035569870.00872261690490.2163449621220.03177644677850.2694708285116.579592831158.4165201206218.274783327
403.168949684791.343852939981.34495145521.266671365990.4281971283831.063892288310.12181912031-0.412586883633-0.06683888657380.0825160864094-0.09968794022620.05773266208470.0449280760769-0.1280536420490.0003924551120240.221817069519-0.01090180242380.0375445237030.200844524857-0.006893701529910.18832137462914.273400891452.507578053213.199840724
411.545893762010.515017855118-1.28454474281.191965016520.0329610582993.20888249807-0.0341406600066-0.0964653074135-0.171148815675-0.2614595387610.00397257869930.07073842368930.0416317118250.3526889118620.009060665308510.287360484184-0.0104726525273-0.01385120088150.1936064333740.03840928963840.317509189033.1222786608542.9978205871196.382430406
421.843640566580.539279892792-0.3358750757581.42242489968-0.3934376125952.805042967-0.191211306426-0.0894570771675-0.263363539286-0.214780758882-0.07805143996150.319116620390.142735734309-0.02866885351490.2557956161130.309136673566-0.01215548443870.02384485256220.2100668965950.02968920536590.3368893405390.81730390661445.3615745257200.191238384
432.4942491136-0.071339497753-0.1924466724692.272006017830.3734776493991.371238336640.2550587952410.195847256264-0.384890751118-0.646151005010.3482994520370.3521965931330.0310181061689-0.22464723651-0.3463514538420.389005482202-0.03384253569920.002352860101080.291417488620.09632007146570.374356079676-8.2139365549736.7432698844200.80313576
441.973590418680.406771180940.7213668169381.307741140210.8885608974771.78470124018-0.1705244568690.4012989138590.184579588692-0.1900486781930.0790765578069-0.0257419210076-0.2399259130490.2611537306570.08925793662450.319913100801-0.0981285469147-0.009687799397130.3829220972940.05572513045870.28008842030234.419088620167.0682769101201.948601593
451.323420258470.399262162044-1.193860157393.288369211630.810897960791.59052603947-0.1214532245380.005908742825050.1743965382220.3421598373470.175103419501-0.154367670445-0.1182967827520.331155885476-0.03158204830120.335116682105-0.029562713933-0.05079907897480.2721815337980.006718918227530.34236687973630.110148921871.6902879864215.03629786
462.073976894930.9679141900371.583789761610.7390187434640.2611439308971.704541129360.2476501667830.199138031176-0.2384524254560.311569433113-0.0364887550809-0.08305680491860.4680852006770.558277197712-0.1604111679760.309583796403-0.004397788913-0.02467440310340.40196221891-0.01598754218720.24793289967726.438858986753.780960878187.440987676
472.35040710392-0.441142335484-0.5407537481730.593693136338-0.696981772731.081764158880.15548591394-0.1958308864010.0497715864142-0.0821555455377-0.07406077464720.0989031549485-0.1655660867370.0440604799429-0.04987881939620.278905495948-0.0483295560544-0.007509975388810.197426535293-0.02385016416630.2263166124792.548677982953.6877555363193.28707208
482.033540334781.16893428742-0.9096168404771.43659554022-0.2898750664933.2046791622-0.0270728986714-0.576264550624-0.05246752126270.236057455897-0.0986486499008-0.254002965144-0.07941861557880.5633506269710.1901331470760.386102109389-0.0643175506904-0.03215907711680.3837640680270.04614498055920.25031653517611.988148780752.3763850586195.625891368
491.30018320482-0.587934027299-0.9830446266380.968707057262-0.0782499251451.109585152070.28655959891-0.273953099924-0.130388047538-0.174832594797-0.07519079085070.161436495939-0.1802266998490.0940490585638-0.2475590428340.309242711467-0.04354772098780.01884705247910.2196347195330.02572006835940.24109314005-1.9382874169755.2647484374196.271616438
503.26064716629-0.7206178836990.0719630945050.478250703950.7486951733671.935189982870.03146523225310.3456404006760.860920830423-0.442209338980.2913727369960.156182032249-0.3580606036220.0745763007104-0.3717767000550.427045594015-0.0686486335451-0.01498108961990.2340197037590.07550188650820.425641420269-0.56877919176262.4139550618188.899088995
512.44768138515-0.841575127169-1.015968024021.24809034860.01010935829031.653009941620.042948344924-0.19165323513-0.134711177566-0.031237537283-0.02129037996340.0233781352387-0.03870408082790.115697661253-0.004862317118680.343068878506-0.0437932312028-0.02520715252020.2713355126490.03609143771140.23017106429915.568855930258.9323456536181.346976682
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 0 through 83 )AA0 - 831 - 84
22chain 'A' and (resid 84 through 158 )AA84 - 15885 - 159
33chain 'A' and (resid 159 through 205 )AA159 - 205160 - 200
44chain 'A' and (resid 206 through 270 )AA206 - 270201 - 265
55chain 'B' and (resid 0 through 11 )BC0 - 111 - 12
66chain 'B' and (resid 12 through 19 )BC12 - 1913 - 20
77chain 'B' and (resid 20 through 30 )BC20 - 3021 - 31
88chain 'B' and (resid 31 through 41 )BC31 - 4132 - 42
99chain 'B' and (resid 42 through 51 )BC42 - 5143 - 52
1010chain 'B' and (resid 52 through 61 )BC52 - 6153 - 62
1111chain 'B' and (resid 62 through 71 )BC62 - 7163 - 72
1212chain 'B' and (resid 72 through 77 )BC72 - 7773 - 78
1313chain 'B' and (resid 78 through 83 )BC78 - 8379 - 84
1414chain 'B' and (resid 84 through 97 )BC84 - 9785 - 98
1515chain 'C' and (resid 0 through 84 )CD0 - 841 - 85
1616chain 'C' and (resid 85 through 171 )CD85 - 17186 - 172
1717chain 'C' and (resid 172 through 270 )CD172 - 270173 - 266
1818chain 'D' and (resid 1 through 17 )DF1 - 171 - 17
1919chain 'D' and (resid 18 through 102 )DF18 - 10218 - 102
2020chain 'D' and (resid 103 through 135 )DF103 - 135103 - 129
2121chain 'D' and (resid 136 through 150 )DF136 - 150130 - 144
2222chain 'D' and (resid 151 through 184 )DF151 - 184145 - 177
2323chain 'D' and (resid 185 through 199 )DF185 - 199178 - 192
2424chain 'E' and (resid 3 through 94 )EG3 - 941 - 92
2525chain 'E' and (resid 95 through 109 )EG95 - 10993 - 107
2626chain 'E' and (resid 110 through 124 )EG110 - 124108 - 122
2727chain 'E' and (resid 125 through 140 )EG125 - 140123 - 138
2828chain 'E' and (resid 141 through 242 )EG141 - 242139 - 240
2929chain 'F' and (resid 0 through 5 )FH0 - 51 - 6
3030chain 'F' and (resid 6 through 19 )FH6 - 197 - 20
3131chain 'F' and (resid 20 through 41 )FH20 - 4121 - 42
3232chain 'F' and (resid 42 through 51 )FH42 - 5143 - 52
3333chain 'F' and (resid 52 through 61 )FH52 - 6153 - 62
3434chain 'F' and (resid 62 through 71 )FH62 - 7163 - 72
3535chain 'F' and (resid 72 through 90 )FH72 - 9073 - 91
3636chain 'F' and (resid 91 through 99 )FH91 - 9992 - 100
3737chain 'G' and (resid 1 through 52 )GI1 - 521 - 52
3838chain 'G' and (resid 53 through 75 )GI53 - 7553 - 75
3939chain 'G' and (resid 76 through 91 )GI76 - 9176 - 91
4040chain 'G' and (resid 92 through 120 )GI92 - 12092 - 120
4141chain 'G' and (resid 121 through 156 )GI121 - 156121 - 156
4242chain 'G' and (resid 157 through 190 )GI157 - 190157 - 190
4343chain 'G' and (resid 191 through 201 )GI191 - 201191 - 201
4444chain 'H' and (resid 1 through 94 )HJ1 - 941 - 94
4545chain 'H' and (resid 95 through 109 )HJ95 - 10995 - 109
4646chain 'H' and (resid 110 through 124 )HJ110 - 124110 - 124
4747chain 'H' and (resid 125 through 162 )HJ125 - 162125 - 162
4848chain 'H' and (resid 163 through 188 )HJ163 - 188163 - 188
4949chain 'H' and (resid 189 through 203 )HJ189 - 203189 - 203
5050chain 'H' and (resid 204 through 215 )HJ204 - 215204 - 215
5151chain 'H' and (resid 216 through 244 )HJ216 - 244216 - 244

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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

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