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- PDB-7umg: Crystal structure of human CD8aa-MR1-Ac-6-FP complex -

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基本情報

登録情報
データベース: PDB / ID: 7umg
タイトルCrystal structure of human CD8aa-MR1-Ac-6-FP complex
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • T-cell surface glycoprotein CD8 alpha chain
キーワードIMMUNE SYSTEM / CD8 coreceptor / MR1 / metabolite presentation
機能・相同性
機能・相同性情報


cytotoxic T cell differentiation / MHC class I protein complex binding / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / T cell mediated immunity / T cell receptor complex / MHC class I protein binding / plasma membrane raft / antigen processing and presentation ...cytotoxic T cell differentiation / MHC class I protein complex binding / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / T cell mediated immunity / T cell receptor complex / MHC class I protein binding / plasma membrane raft / antigen processing and presentation / beta-2-microglobulin binding / coreceptor activity / T cell receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region
類似検索 - 分子機能
CD8 alpha subunit / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain ...CD8 alpha subunit / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Chem-30W / PHOSPHATE ION / T-cell surface glycoprotein CD8 alpha chain / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
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: 2.4 Å
データ登録者Awad, W. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC)DE220101491 オーストラリア
引用ジャーナル: J.Exp.Med. / 年: 2022
タイトル: CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells.
著者: Souter, M.N.T. / Awad, W. / Li, S. / Pediongco, T.J. / Meehan, B.S. / Meehan, L.J. / Tian, Z. / Zhao, Z. / Wang, H. / Nelson, A. / Le Nours, J. / Khandokar, Y. / Praveena, T. / Wubben, J. / ...著者: Souter, M.N.T. / Awad, W. / Li, S. / Pediongco, T.J. / Meehan, B.S. / Meehan, L.J. / Tian, Z. / Zhao, Z. / Wang, H. / Nelson, A. / Le Nours, J. / Khandokar, Y. / Praveena, T. / Wubben, J. / Lin, J. / Sullivan, L.C. / Lovrecz, G.O. / Mak, J.Y.W. / Liu, L. / Kostenko, L. / Kedzierska, K. / Corbett, A.J. / Fairlie, D.P. / Brooks, A.G. / Gherardin, N.A. / Uldrich, A.P. / Chen, Z. / Rossjohn, J. / Godfrey, D.I. / McCluskey, J. / Pellicci, D.G. / Eckle, S.B.G.
履歴
登録2022年4月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年8月3日Provider: repository / タイプ: Initial release
改定 1.12022年9月7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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22022年9月14日Group: Database references / カテゴリ: citation_author / Item: _citation_author.identifier_ORCID
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
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD8 alpha chain
D: T-cell surface glycoprotein CD8 alpha chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,7957
ポリマ－72,4324
非ポリマー3643
水2,324129
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: surface plasmon resonance
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-49 kcal/mol
Surface area27140 Å2
手法PISA
単位格子
Length a, b, c (Å)166.495, 166.495, 166.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDモデル要素
11A-471-

HOH

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要素

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タンパク質 , 3種, 4分子 ABCD

#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: 1 / 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: 1 / 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 T-cell surface glycoprotein CD8 alpha chain / T-lymphocyte differentiation antigen T8/Leu-2


分子量: 14420.284 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: CD8A, MAL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01732

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非ポリマー , 4種, 132分子

#4: 化合物 ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin / 2-(アセチルアミノ)-4-オキソ-3,4-ジヒドロプテリジン-6-カルボアルデヒド


分子量: 233.184 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C9H7N5O3 / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 1 / 由来タイプ: 合成 / 式: PO4
#6: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 129 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.65 Å3/Da / 溶媒含有率: 53.67 %
結晶化温度: 298 K / 手法: 蒸気拡散法 / 詳細: Na K Phosphate, PEG 1K and NaCl / PH範囲: 6.0 - 6.5

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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: MX2 / 波長: 0.954 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年6月21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: 0.954 Å / 相対比: 1
反射解像度: 2.4→48.07 Å / Num. obs: 144365 / % possible obs: 99.82 % / 冗長度: 4.8 % / Biso Wilson estimate: 58.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05795 / Net I/σ(I): 17.41
反射 シェル解像度: 2.4→2.49 Å / Num. unique obs: 14865 / CC1/2: 0.683

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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
XDS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: 6PUC

6puc


解像度: 2.4→39.24 Å / SU ML: 0.3681 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.9528
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2183 3792 6.56 %
Rwork0.185 53975 -
obs0.1873 57767 98.51 %
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: 67.24 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→39.24 Å
タンパク質核酸リガンド溶媒全体
原子数4702 0 22 129 4853
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00324969
X-RAY DIFFRACTIONf_angle_d0.66046787
X-RAY DIFFRACTIONf_chiral_restr0.0418718
X-RAY DIFFRACTIONf_plane_restr0.0048893
X-RAY DIFFRACTIONf_dihedral_angle_d14.88391783
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.40211300.33331927X-RAY DIFFRACTION91.79
2.43-2.460.38151450.29852028X-RAY DIFFRACTION98.86
2.46-2.490.32311380.30371970X-RAY DIFFRACTION98.23
2.49-2.530.28091390.29472020X-RAY DIFFRACTION97.69
2.53-2.570.35331420.27911951X-RAY DIFFRACTION97.48
2.57-2.610.30451400.27262011X-RAY DIFFRACTION97.55
2.61-2.650.2911320.27591939X-RAY DIFFRACTION98.48
2.65-2.690.32011460.26631938X-RAY DIFFRACTION98.39
2.69-2.740.29791400.27572039X-RAY DIFFRACTION97.93
2.74-2.80.33231400.26921988X-RAY DIFFRACTION97.84
2.8-2.850.31641370.25011993X-RAY DIFFRACTION99.49
2.85-2.920.25251450.24042051X-RAY DIFFRACTION99.73
2.92-2.980.26491390.23671999X-RAY DIFFRACTION100
2.98-3.060.26941560.21162059X-RAY DIFFRACTION100
3.06-3.140.2871340.20612008X-RAY DIFFRACTION99.91
3.14-3.230.24641390.22182026X-RAY DIFFRACTION99.95
3.23-3.340.21611450.2042003X-RAY DIFFRACTION99.63
3.34-3.460.26251470.19532025X-RAY DIFFRACTION98.95
3.46-3.590.24591410.17041996X-RAY DIFFRACTION98.62
3.6-3.760.20391360.16811974X-RAY DIFFRACTION98.32
3.76-3.960.21781380.15831976X-RAY DIFFRACTION97.92
3.96-4.20.17281420.14422004X-RAY DIFFRACTION98.94
4.2-4.520.16611360.13372009X-RAY DIFFRACTION100
4.53-4.980.15191330.13452042X-RAY DIFFRACTION99.72
4.99-5.70.17291420.15262009X-RAY DIFFRACTION99.54
5.7-7.150.18891390.18551990X-RAY DIFFRACTION98.43
7.18-39.240.17711510.16342000X-RAY DIFFRACTION98.44
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)
11.027748359920.100127697259-0.2019402343040.139650932394-0.3252951642460.634309820787-0.1950681876410.04605924445670.01864424987550.0167580977370.2580662738650.2809139801650.2277156985840.16496054962-0.0001013655249790.397494407511-0.000666857843376-0.07247908424810.422466758032-0.02003916077820.43157108959917.7154.435-45.974
21.7799395283-0.7702303709230.8943295195570.477707926884-0.4796901426850.570406426921-0.0126439754950.1399082441880.0913846567556-0.2089873705060.05881580722820.0304156979378-0.2223336377790.214050077087-6.78913653224E-50.479665474565-0.03329401136980.0008048289221370.396461134585-0.03079751062870.38214692407823.93760.553-52.732
31.125622200760.5212796506360.007940351706172.52310480465-0.09645993502461.615384626650.0940838412913-0.0108265959038-0.1756830487230.227576421553-0.0174428738489-0.1309480480530.1378457178440.06910337593851.2051426798E-60.3664638262060.0136269355082-0.1071610386490.393209823919-0.03060722671310.40358361191422.9647.669-41.031
40.295755048532-0.289594162010.2334258955020.297196539126-0.01518506931021.111550861420.18184110057-0.00810224150696-0.4075225301310.612100152332-0.0271007960064-0.1640677091720.08598317727050.5099421576811.62577344373E-50.553962003270.0483572731792-0.1519908123930.546054740818-0.01060847915420.63099812658730.00144.416-33.639
50.9489514744190.991987240568-0.5931522942661.0757484626-0.07784113559561.44687076410.2097335780270.05425253330230.595500370549-0.214007868706-0.414294643294-0.30431205022-0.1712689790870.163913632526-0.00058023299450.361219344689-0.0932487368102-0.07810655783940.448359616111-0.04593525431580.51251401142225.5571.399-42.793
60.351904137905-0.196132764001-0.6015311596550.2620145898910.6148828141081.0240131354-0.477983628070.3497472066020.132124706793-0.1070675038760.2269570925320.08934097504730.397501714062-0.25964016139-6.18069403968E-50.377894532863-0.01812751599620.002301031460910.467401268138-0.01081377102790.553028678084-10.10474.396-38.905
70.4080012156020.5903841190440.01225186080.6632141584410.1608720935930.09627183059310.108662412287-0.283685456093-0.639896043740.218022313355-0.43703931529-0.09623951548550.09303979076430.0242673230407-0.000180608952290.518032462060.00956560542225-0.03713599027180.484838690826-0.006201202465890.5122036573454.24374.146-34.306
80.9072794084830.1590975923460.8927576550.2776596790540.3037837157010.8772257434380.0471989207685-0.0917166068324-0.05066955134030.0209797085456-0.04022536250970.09126449364090.2305226898380.168662520328-0.0001188284803290.4046304332510.03736528027980.01266997858290.333891067001-0.00611816025550.5721000233160.60269.881-36.226
90.303681637806-0.0437219799940.2683783013840.05129085554420.009063825836140.242806813434-0.0438841442209-0.0554635124001-0.0165572934160.228199054309-0.2072567768440.0882801017049-0.23133963074-0.738378801667-7.08509530943E-50.497776861254-0.01749443108580.1127849265080.582710033306-0.04035987819840.528064735093-12.39972.631-29.666
100.219900176008-0.3940264380360.2724127146870.419257256553-0.3605717553780.605311254506-0.190881167956-0.05402718916220.204958247310.291852231150.17794743084-0.2387670534230.02965744991620.0271911544072.84828222915E-50.479337879179-0.0210177868108-0.04229858392980.530168550407-0.07583220903910.5983645404086.33176.153-32.956
111.887632108640.6013151059420.7219519921810.490080953424-0.3847367973060.252008615495-0.0239900471422-0.04143961356290.07260028465290.3982978163820.1744853529540.344815036322-0.192686524724-0.06067041476590.002971336160430.378743783469-0.0202446648163-0.0190077686270.4213802172280.05836731342670.5352333626470.30665.193-50.131
120.8661694073410.499493440649-0.1945063802580.7616602963110.3791255712170.4120192700960.4685229587280.72109938009-0.892970025916-0.6555617807980.04899000834420.9735064174480.5842754083070.2030944092430.0009628856523560.572121392683-0.00387637005462-0.2478565656040.5210225786920.007909015960340.635923448143-0.96856.707-57.642
130.00954473096132-0.0506799187124-0.03026181872830.08260455795170.05130853081280.1020909241190.402758502062-0.0835485273605-0.263490297871-0.2896580523510.18991019451-0.388335730731-0.280661831524-0.08469070971032.342881942350.855190097337-0.0141540321066-0.05418393495270.82764800562-0.01324588456290.4211072279895.41263.098-62.502
140.6596097301810.9739708250290.1162980389211.749311899860.6930454508190.9246572578770.1976934528770.373550156919-0.0186072118345-0.1420114217730.0790225321404-0.1520798672080.1916879614590.37256363190.0001867362816950.359867691708-0.00559415094837-0.01868861393230.4729085151430.03743328736430.4876005329444.45462.515-52.206
150.297315293483-0.3240458112020.1490284842610.299462004294-0.0371882951961.20426339813-0.09179465015780.39363487311-0.408234189539-1.279183604210.8598443333830.7274595109930.788460701363-0.1467123284460.06741046849120.505012133596-0.147227084081-0.2010439278610.5345119627260.1391174585390.816608342184-4.30452.774-53.632
160.03864664985920.291880485343-0.2938180708213.86067171671-3.893137818793.924993424020.1110444607280.395557949892-0.3986199544891.267029857550.9755263713690.753573490247-0.985716973927-0.6711156475640.1526149037580.47170445659-0.02262962763440.1045464615590.6393999066890.12793010870.958528372769-9.06566.18-50.257
171.85016542282-0.300251152244-0.8587505931691.393418887010.8561282734611.58187045254-0.158778090228-0.07062410909820.1438007993280.2039049680010.225315504652-0.609229395068-0.197737848851-0.1133775553580.0790257896740.6282914861920.0827817378152-0.1240740953610.701080443303-0.1462825652110.87581311335611.12655.684-20.053
183.98145896619-0.392363388939-2.085479065220.747916192988-0.3641108842341.543981351641.41053715711-1.377550382641.224908405460.2855766991670.629106580254-1.164470223880.451503414233-0.6029320579420.2681816267751.229879673610.0575975285356-0.2850542952071.09094187737-0.184482147311.1727320437411.8564.537-8.736
190.1355497201790.0988852587987-0.03735831691420.2552907473390.09398348340680.0814229298304-0.298719248607-0.4538431288340.780102823652-0.1992232317060.540731127824-0.862848018642-0.469311098747-1.19967226080.0005738402843770.7890799023460.119210033117-0.1675576941390.791130691578-0.1505426981511.0205698678215.74661.812-20.391
200.0468258474363-0.04411030800710.04642757823940.0273663742568-0.02186664477010.0420588251111-0.678260175534-0.9270220742871.130425220490.360795476309-0.0730582914586-0.132774400479-0.02348874031510.222115662937-0.000789243266351.335773887760.0394629267801-0.4257505916321.289278368820.0595832546471.2042177375517.6951.592-5.867
210.2023750729930.4558645094030.1807999051220.9252547079440.1089239365110.539317946580.339602809040.0364615589556-0.0608688138955-0.2895991934710.464501276308-0.6324875512770.473443534366-0.349510419560.04840096218220.5618988293140.0371681152303-0.1192016271050.683639718648-0.0334815056640.8703176612326.88252.085-20.822
220.551424211915-0.366572944470.138150159250.54510374657-0.4159966738010.39330989346-0.56904852709-0.960093395294-0.7023914569980.2826012513010.7671066620440.785807238819-0.180931705184-0.69457208067-0.003895199991090.885447402508-0.02937051740090.1069249459880.936997115940.1892770640971.24289187204-15.41845.765-11.742
230.402229728365-0.3085726951690.4055500255170.305490894249-0.3123138836890.384532966349-0.948976905443-1.088665193680.00603816833161.371087520760.4385137314720.8507955851540.271321970030.332482517507-0.05633223812040.686157128434-0.03902244249140.1355193196010.5927589743150.1293559043720.700980534996-16.48952.458-14.325
24-0.003007775951040.00594541311451-0.0130180069013-0.000682766000537-0.01354919115470.02073621540420.335783528890.4584986042610.564904269717-0.4723528909210.4434616710040.425245791506-0.1182888114150.5966247316580.001005465011831.2206059071-0.02738231410070.0701733328120.6192998517620.01413133544790.96872047873-10.19466.005-12.841
250.4047741855250.191725976018-0.3490012002120.393927950309-0.3576795478790.2746722658350.0917044324260.269384798152-0.601683868168-0.1558700774250.2257922972190.1609525269460.1395436761370.1509794414145.49724230427E-50.673223708152-0.00555135706504-0.01332910442410.7174662887720.02824761025070.852819735253-8.63151.765-24.548
260.217770735667-0.09148588759340.09749484651040.087806210072-0.1222467254010.152838774770.1051758979950.09462785144590.1934530997380.217732484703-0.0676905440888-0.450331154997-0.2090586359340.1535689378212.17127436253E-50.7379440410070.01574868693450.03334212446710.7532947468270.01554393772260.907875249643-17.98354.734-19.891
270.15758080614-0.0132503988556-0.1980366917870.0886563580712-0.03206253739620.205755450782-0.5199510185630.4442538524-1.27373879467-0.780501174832-0.0704037370943-0.1889745472310.672127340403-0.16806369874-0.0002385285596090.9015176127370.1175009337270.1235697844740.689134222471-0.1216913691271.76275745132-12.82137.402-23.419
281.40592952366-0.7720618758050.2787688460070.4292652833320.04658174605290.531439002885-0.739832701836-0.298913059325-0.2939158793070.1501755291491.22611070270.3006835056320.0736120016748-0.1576103876030.0003149472256980.6964520886180.0453817167830.04538400552730.8270075044670.1722004258850.84200883831-6.22751.728-13.911
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:21 )A0 - 21
2X-RAY DIFFRACTION2( CHAIN A AND RESID 22:55 )A22 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:133 )A56 - 133
4X-RAY DIFFRACTION4( CHAIN A AND RESID 134:158 )A134 - 158
5X-RAY DIFFRACTION5( CHAIN A AND RESID 159:182 )A159 - 182
6X-RAY DIFFRACTION6( CHAIN A AND RESID 183:203 )A183 - 203
7X-RAY DIFFRACTION7( CHAIN A AND RESID 204:216 )A204 - 216
8X-RAY DIFFRACTION8( CHAIN A AND RESID 217:239 )A217 - 239
9X-RAY DIFFRACTION9( CHAIN A AND RESID 240:253 )A240 - 253
10X-RAY DIFFRACTION10( CHAIN A AND RESID 254:265 )A254 - 265
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:30 )B1 - 30
12X-RAY DIFFRACTION12( CHAIN B AND RESID 31:46 )B31 - 46
13X-RAY DIFFRACTION13( CHAIN B AND RESID 47:51 )B47 - 51
14X-RAY DIFFRACTION14( CHAIN B AND RESID 52:77 )B52 - 77
15X-RAY DIFFRACTION15( CHAIN B AND RESID 78:90 )B78 - 90
16X-RAY DIFFRACTION16( CHAIN B AND RESID 91:99 )B91 - 99
17X-RAY DIFFRACTION17( CHAIN C AND RESID 1:56 )C1 - 56
18X-RAY DIFFRACTION18( CHAIN C AND RESID 57:67 )C57 - 67
19X-RAY DIFFRACTION19( CHAIN C AND RESID 68:81 )C68 - 81
20X-RAY DIFFRACTION20( CHAIN C AND RESID 82:89 )C82 - 89
21X-RAY DIFFRACTION21( CHAIN C AND RESID 90:113 )C90 - 113
22X-RAY DIFFRACTION22( CHAIN D AND RESID 1:17 )D1 - 17
23X-RAY DIFFRACTION23( CHAIN D AND RESID 18:24 )D18 - 24
24X-RAY DIFFRACTION24( CHAIN D AND RESID 25:32 )D25 - 32
25X-RAY DIFFRACTION25( CHAIN D AND RESID 33:67 )D33 - 67
26X-RAY DIFFRACTION26( CHAIN D AND RESID 68:81 )D68 - 81
27X-RAY DIFFRACTION27( CHAIN D AND RESID 82:89 )D82 - 89
28X-RAY DIFFRACTION28( CHAIN D AND RESID 90:113 )D90 - 113

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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