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- PDB-9cgs: Structure of human MAIT A-F7 TCR in complex with human MR1-Pyrido... -

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基本情報

登録情報
データベース: PDB / ID: 9cgs
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-Pyridoxal-5'-phosphate
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR TRAV1-2
  • TCR TRBV6-1
キーワードIMMUNE SYSTEM / immune receptors
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 / : / : / positive regulation of receptor binding / early endosome lumen ...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 / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / 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 / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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
ACETIC ACID / 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 Å
データ登録者Awad, W. / Rossjohn, R.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC) オーストラリア
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2024
タイトル: MR1 presents vitamin B6-related compounds for recognition by MR1-reactive T cells.
著者: McInerney, M.P. / Awad, W. / Souter, M.N.T. / Kang, Y. / Wang, C.J.H. / Chan Yew Poa, K. / Abdelaal, M.R. / Le, N.H. / Shepherd, C.M. / McNeice, C. / Meehan, L.J. / Nelson, A.G. / Raynes, J.M. ...著者: McInerney, M.P. / Awad, W. / Souter, M.N.T. / Kang, Y. / Wang, C.J.H. / Chan Yew Poa, K. / Abdelaal, M.R. / Le, N.H. / Shepherd, C.M. / McNeice, C. / Meehan, L.J. / Nelson, A.G. / Raynes, J.M. / Mak, J.Y.W. / McCluskey, J. / Chen, Z. / Ang, C.S. / Fairlie, D.P. / Le Nours, J. / Illing, P.T. / Rossjohn, J. / Purcell, A.W.
履歴
登録2024年6月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年11月27日Provider: repository / タイプ: Initial release
改定 1.12024年12月11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
改定 1.22025年4月9日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg

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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 TRAV1-2
E: TCR TRBV6-1
F: Beta-2-microglobulin
G: TCR TRAV1-2
H: TCR TRBV6-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,97614
ポリマ－188,5568
非ポリマー4196
水17,240957
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR TRAV1-2
H: TCR TRBV6-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,5458
ポリマ－94,2784
非ポリマー2674
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: TCR TRAV1-2
E: TCR TRBV6-1
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,4306
ポリマ－94,2784
非ポリマー1522
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)216.801, 70.076, 142.880
Angle α, β, γ (deg.)90.000, 104.551, 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: 31939.787 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 TRAV1-2


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 TRBV6-1


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 , 4種, 963分子

#5: 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: 3 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物 ChemComp-ACY / ACETIC ACID / 酢酸


分子量: 60.052 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H4O2
#7: 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 / 式: Na
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 957 / 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
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: 2.84 Å3/Da / 溶媒含有率: 56.71 %
結晶化温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG 3350, BTP, Ca acetate

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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: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年4月22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→44.18 Å / Num. obs: 138487 / % possible obs: 98.48 % / 冗長度: 3.4 % / Biso Wilson estimate: 37.67 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.05
反射 シェル解像度: 2→2.07 Å / 冗長度: 3.6 % / Num. unique obs: 49319 / CC1/2: 0.781

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.1_5286精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2→44.18 Å / SU ML: 0.2325 / 交差検証法: FREE R-VALUE / σ(F): 1.49 / 位相誤差: 23.6549
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2 1998 1.44 %
Rwork0.1733 136322 -
obs0.1737 138320 98.52 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 49.37 Å2
精密化ステップサイクル: LAST / 解像度: 2→44.18 Å
タンパク質核酸リガンド溶媒全体
原子数12760 0 57 957 13774
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002913412
X-RAY DIFFRACTIONf_angle_d0.64118304
X-RAY DIFFRACTIONf_chiral_restr0.04531955
X-RAY DIFFRACTIONf_plane_restr0.00442380
X-RAY DIFFRACTIONf_dihedral_angle_d14.27974844
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31391410.31279579X-RAY DIFFRACTION98.29
2.05-2.110.28081420.27619650X-RAY DIFFRACTION98.43
2.11-2.170.29221420.25479703X-RAY DIFFRACTION98.73
2.17-2.240.26371430.24299721X-RAY DIFFRACTION98.74
2.24-2.320.26841420.23479716X-RAY DIFFRACTION98.81
2.32-2.410.25251440.22599791X-RAY DIFFRACTION99.02
2.41-2.520.25411420.21899719X-RAY DIFFRACTION99.05
2.52-2.650.27461430.21769790X-RAY DIFFRACTION99.09
2.65-2.820.24981430.20979778X-RAY DIFFRACTION99.17
2.82-3.040.20871430.19519777X-RAY DIFFRACTION98.9
3.04-3.340.19961430.17459741X-RAY DIFFRACTION98.15
3.34-3.830.20131420.14649671X-RAY DIFFRACTION97.85
3.83-4.820.13191430.129778X-RAY DIFFRACTION97.99
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)
11.65649119885-0.201985708325-0.2608603142831.341668127010.9960109707821.611328619320.05606407671240.1013540046220.162551603791-0.1341087033510.0272588026615-0.1509184512620.006791321559620.135489214849-0.07171812547330.208625703956-0.0181351120906-0.003826917206710.292873525193-0.009683179221850.3164814029149.660461494677.905546206223.633929448
21.482982393660.125936467659-0.01963331460442.39993880560.2406700872770.8647403024520.0472534999537-0.1305540681740.1235872751020.0969077564473-0.03410525175690.177290062855-0.0449648346125-0.0804956803146-0.01955462978390.249141580556-0.0003775931666170.007084688557840.277318988055-0.01604651085280.31230095448137.174988326981.0670976999234.133093857
32.33310238591-0.5924507079670.7024635291281.024714814540.3365636715011.457777161720.0468671881191-0.00959138159057-0.1547082758590.161285980670.190839674098-0.3165438891350.08661494196770.243982772101-0.1960736365420.2980308611040.0259416218174-0.04053472292570.357044484297-0.01393641135490.34570042305962.420730385571.083037482242.91471943
41.479819289680.496501554536-0.2300498431461.107202205290.02444950007361.34620495093-0.00337215145747-0.2629213925320.4333852220980.3018600730120.00928548520741-0.0447341369572-0.328142383518-0.113534122123-0.02905940075740.4034997208450.108591376458-0.1017988285990.558660031403-0.1677784499310.49716303119466.598646656380.2883300552256.257821594
52.42258102664-0.392113099998-0.2317543247872.02050673112-0.2314973452731.2421531648-0.055631836957-0.1218944237060.2074710459280.1390379311790.02302228202780.045664818185-0.2344903002040.01798822068490.01377515402560.417437612372-0.00261054602229-0.08122405172920.468119957918-0.1081809900630.62975353919260.790342819592.8042909116237.589315989
62.837521125091.97599069653-1.505428149691.907473031710.2627770469453.94546335774-0.498524794847-0.362792688228-0.06910725741820.3812265087880.0687397485428-0.9575824367360.2062288063090.83049024140.3095759316510.4121421083780.0200102476647-0.2240453822530.847883189652-0.01848090319810.90562073393582.057084618379.9897485741240.610017033
71.99735011106-0.06553855509070.09544529645770.6923290949220.07788066417120.882134111553-0.09111803444530.2504392527320.132809311665-0.1465012945880.118780648966-0.323463080175-0.1079777276720.428707651732-0.01072992756940.357710687884-0.0853901043061-0.04266090582350.537688790212-0.01325473442670.62344962282567.516039268589.1896712599232.263847903
83.399557130760.926918812649-0.9581972483453.5496810529-0.6710787248371.658384169240.1636127314250.3335011958610.020210707533-0.444382641133-0.373526019928-0.32057260496-0.05871456466950.315013906510.1709792492220.42562446914-0.06847135157180.01216444445190.841051294616-0.009013576527480.76643888124475.68279277489.5717061772226.400233329
96.85065218158-1.54065037393-1.942737407082.205827820450.651593232892.269888100210.141206338758-0.1187176675240.302782583360.0413555746270.0364559449527-0.247803436254-0.09171587621320.42468211777-0.01647565963360.333809840329-0.0189166553822-0.01624109577550.375883403904-0.02596085976610.4171310662954.259656064384.1705373016232.880391408
102.02876248186-0.2457044492160.9710685537970.201105013483-0.3910778840860.80531016619-0.5747964743971.18816878765-0.259372216030.001040423621320.213150148148-0.3287883677510.0479825645960.3751527152070.3373960195130.348602548181-0.02756884190950.0310850493710.536714826016-0.05966873658630.57638462373470.064739469584.2709099426231.71494165
110.3080528036180.04082971249660.0169535517570.05853763326610.2543366290091.26138076605-0.06827017977570.1253904720970.2975099098990.02504950254020.172145525006-0.240968533635-0.2786385928960.3778956891770.02959723475830.415790823964-0.0184057180977-0.2218744057811.33774900011-0.1390487948181.1953163506686.46180911290.3818777365237.373670136
122.772360919130.901750632016-0.4537074371960.7104694047360.7004594171581.78181986090.467883858425-0.2327725812210.231474300588-0.0411711485754-0.2818354461-1.09178047837-0.2288668504780.634627840907-0.1321282221640.469863934456-0.141820275625-0.07680106133460.6791133185470.1503582592651.0605301287572.083278894994.9902580543232.295035317
133.54927412025-0.644471870111-1.205949695912.4598686418-1.375998678681.719753375350.239457648105-0.2397482214550.5632875183780.2439182618520.124997819507-0.4681605808-1.088980045010.642215500121-0.2991708954650.563928431517-0.0921931258052-0.01812084553780.507123327747-0.01966890163210.87012135067661.5408099222101.834666908231.889952151
144.93740610445-1.737738483210.5103178207014.17353493392-0.2670568851263.37981481734-0.0256428056901-0.379962250594-0.1183566570580.6017165265110.477517870353-0.2018818284770.1010522960920.548674169533-0.3847495033720.526148377148-0.0785271833749-0.2045180389210.735338743619-0.1572311335080.86669948765475.220973477793.4989737962240.137856142
151.36478715505-0.02167563262030.04210227118171.75115597181-0.3321875451952.095054315670.01627507435790.2316211478290.0495873329676-0.0878695959232-0.1307621963390.207110975813-0.07348468017030.01374672199990.1061717171880.297028454853-0.01492857027830.01582143048920.363619109392-0.02272483584180.311141112047-4.9612402668863.5482497339159.983289278
161.54746355296-0.3638343578640.1446671785841.66063068347-0.7423319437150.9117226575190.0550401468071-0.00887437092655-0.05131222683580.148894083102-0.140472249065-0.05923108287230.0115704275130.1696852122870.1070147754830.310126817103-0.04413027559280.01592681285380.376134912316-0.02442889889220.2419725917492.5892835169555.9068426547170.074083471
171.539554897890.427163653542-0.07050062300861.064394138690.08074250306571.320592182780.00748853407365-0.148011547764-0.129958683281-0.00440580647072-0.05179436803820.0843748184876-0.00842936329002-0.05455372042130.05840008788090.3500642772480.009240757153380.02558144593470.206601038407-0.01869718944380.352340964464-20.972498882772.5355253841188.527157162
181.8544270456-0.0833174377530.5543894756442.37498912893-0.0462726373931.550699200210.0861469483366-0.238286512876-0.09313659834330.235974629415-0.007061933620840.14351226671-0.0150137233754-0.147454460886-0.0920181477550.3849808441610.02387801985220.04988288063840.267954638012-0.01332398487090.361012894693-21.093285736673.3403822781195.205700212
192.935572428580.03125897418430.1783417364071.56254764947-0.5049852477552.183836476760.112614782876-0.123288545921-0.276210193690.0444535812984-0.02772985104140.122161414245-0.1443478140820.385024953116-0.09689911063970.351432308957-0.0619220506317-0.03341289768820.5270037961110.09365236688730.34950355031535.639152136666.4806837712157.041648952
201.283917436270.1826988442790.2561525551790.800887079224-0.1875590346660.6944509769-0.09612982609640.06946118198740.0301771946498-0.1276107502370.0342516407301-0.0614888124595-0.06091473127160.1927121659160.07195897479280.340552273679-0.05601933146330.005242414744810.4486444503570.06281667347580.29679313365925.062347790961.9580990966158.228072959
213.107613516270.144205758849-0.2808340785870.777788208912-0.7936245417982.332313082360.0670732640979-0.0618913849045-0.1340061040640.0512229988452-0.03944972408670.06340612625540.1724553079560.1063652029160.001829848379610.357101397632-0.0466666280622-0.01134974203390.4868652748960.07585093659670.33571135390428.959979401560.4691380426166.075377491
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231.60461197798-0.19499221678-1.089171463931.312211009780.8830099035212.73512842893-0.193806407149-0.205954530025-0.663606053774-0.230021552566-0.188389346872-0.0613426677046-0.03448031836221.037064428990.4304376782980.537194831655-0.0240489935114-0.0117677372030.9690040346460.06009778627930.6509707436458.143132667257.9823630483138.651110011
242.469029682280.71558229318-1.054378410051.741971005481.3113674374.14692279183-0.12788863812-0.07958146197220.660840460289-0.5097840810580.7210755703530.0585581676766-0.8937403038150.223385926839-0.7370671742670.926755330352-0.02826362544880.03540107760370.855230770723-0.01036831070630.76627128112753.245640136768.2453309351141.110865567
252.92491172754-0.245008245218-0.2964148823930.9546660896110.608684751362.20818786321-0.00744016811464-0.03805732298120.056327041959-0.08803407929980.443999861009-0.1036230362570.288121345990.225672898378-0.3693936995970.650712812218-0.0596915166505-0.03954768862340.6641626375790.08756730743260.50868360799751.123948960957.5568928212140.13630827
260.986931242875-1.31928434611.817058784451.7884347634-2.445561939413.353474141340.4168757970110.3866885556420.446820111112-0.7921487110720.541094507735-0.204788845295-0.8969478565670.177520853402-0.8621199763131.12855307075-0.3029425678060.2963895712691.114376530520.09161074631451.0216216503659.139665536370.3074856335127.258009432
272.23136069570.615930346808-1.118611342972.276743307421.439013739455.00072936028-0.4453388092530.2796745967130.557538660136-0.2391415409360.218366098963-0.781974925301-0.01045723024941.25932706890.04211592685760.655017657051-0.09635996103080.08609152404991.00945621530.0076624389050.68572986237462.669518624266.9515147085140.300133579
282.32670981348-0.110008400778-0.8236490453451.37279260959-0.08062498996172.48105064829-0.004768114338110.2768362532960.0457070868704-0.269478612726-0.1109531721160.05551364024-0.0429709857339-0.1788595458550.1274872308070.396518166177-0.0481436703204-0.03325022392170.4871754384690.03945307745520.27131730783214.248648497362.2824465113138.672508882
292.154996097610.8822086296191.436913365872.4877668912-0.1659835906771.30349237870.294812073329-0.593831532594-0.1758793696190.144014971319-0.1520955807180.149988769135-0.0250385789316-0.712704477764-0.2567943484590.362347802821-0.05312444266860.001853005520690.5230802499640.04563959359070.33185472317714.761841871655.7602955187152.121938615
302.71024599899-0.446857064138-1.643322734080.6105907158020.6510224976951.274487715740.0806846295595-0.05585511583490.4024171240240.00719891893760.195006218242-0.0147680216041-0.0312405121789-0.0230215923602-0.177423853540.542709969817-0.02851400979940.05879046313040.621809955560.0874193975520.35905730946128.801218188366.550971271124.379164266
312.566237754790.8069279450250.7991952807140.3610372919650.5430301210951.10872442720.1690559826370.556375738103-0.316560907823-0.2011771007560.0538151050382-0.4997765383860.05492728585511.06351270701-0.1878396102030.584371173590.174675120576-0.01744435858860.897922525436-0.1236414635190.59070991880458.099009347153.3516362627131.665450379
322.911498910380.7143464329091.547567387950.836282808256-0.5172291227332.920001345780.2594066655690.327269292426-0.560210129395-0.05328543740020.09623987448370.02397570556460.2746947875380.466243737028-0.3098393354680.6046570930590.0279897941122-0.003487093618460.558441662663-0.05357407821630.42024301835144.544980627255.0543272127130.919420268
334.187506145010.144982652071.480997001462.300527344630.1353349635743.528960430480.3638158979990.549064472452-0.0733156861009-0.8079945540050.16044191370.1122699205690.09181044238450.330581828941-0.2489169822660.773728363133-0.0774896943212-0.001908208016220.793072864383-0.1002220555010.42002484329734.818146930956.7335271263118.50287055
342.063594117040.1924241458260.4261257094622.207209836950.516449378971.90498200082-0.03884986339640.1640263192860.2642929693630.00687377917126-0.0774788696171-0.0147600173895-0.194439893772-0.2250680517590.1232911894770.3708968171440.00153705672826-0.0187364561340.3016012053-0.02958113327070.39450468487-27.056856713166.6478391714175.017452448
351.81803835713-1.28101316857-0.4384018626994.417361323531.670473107761.25885829044-0.1480954600650.2147088804710.250228163456-0.0737581917009-0.0518172913510.259569219581-0.408517995452-0.2949452327220.2358600563750.3668281876640.0312960459038-0.006316069902350.278218373977-0.0170143441710.360788789725-25.728866966569.2605886172171.839751628
366.22816242105-4.79879976541-0.6198168548863.964515745050.4874804885610.8154041165660.381419034870.934827247988-0.256027800667-0.706382386062-0.4424797461440.431897553108-0.326659628187-0.06325669319630.09901696674630.4458930560360.0173382408305-0.1003292909510.48602067258-0.03837578525650.418222312823-27.058864158361.2329036957164.288475854
375.8052986889-0.5890351097810.6051360860922.70330506186-0.5062362906260.981398066971-0.06009594658670.9508495854210.477059097454-0.570061457303-0.01798052992070.247131228017-0.2486194321570.0111712930350.02716552590410.5207007302360.0178313237591-0.06126052620920.491378112673-0.01767376637850.371935428852-26.614467888868.9781400075163.132220364
385.11913733307-2.424789581440.1983061497522.269525101990.01448211606541.72021363144-0.04046276732780.2790890576750.356932695571-0.3477819371320.0499848192047-0.247861129751-0.223488600260.05736032883170.02218041175040.39312842369-0.0485317235254-0.0004242389382430.325461110582-0.02427963857540.295837159148-21.135635892366.7454293844169.548806169
392.94534417781-1.80414308572-0.6867516061145.172760791150.9939460629261.27929085840.04220784754470.333432396019-0.219665189417-0.459081186449-0.2084465276120.69735010907-0.121617373763-0.3152927417250.1778741380450.350954258255-0.0234102002695-0.1055770115180.397973049796-0.05258413804840.48254057471-34.331086328162.3519982194168.553912161
402.23174104502-0.678211489447-0.4517460769655.761716883312.441612657733.641973908850.059599877379-0.6432949804720.3580452506180.508135643332-0.1532241692620.257327058812-0.233724015503-0.2989561640710.1149100214110.402424347418-0.02624518627590.03494906401490.528943392192-0.08052191147830.437311067299-35.649889958866.9506919876176.951747747
411.48366076160.4931356833460.009210014471261.739062842610.3613899545251.42204709807-0.001026551847080.0635276872732-0.0889306159059-0.000970508460790.154560508672-0.03853950850420.1197664086910.0477457239956-0.1438589082810.284567267843-0.0299177044175-0.008888528309160.2646603722210.02873391738270.32431831826223.310395081457.5875196734220.978409919
425.778065314650.03008784283972.137174258181.99625143460.6266681206663.02996691380.0521376587045-0.4777163541410.1463175646620.0490852429502-0.0429623073290.103512606207-0.013022025979-0.337677327356-0.02607824972940.355076131823-0.04585732167550.02438593054540.291825591730.01167722663240.37763163140820.266576537359.5352923214229.318512076
433.323511886060.5689519512380.382258257911.389477412750.6026776115791.5643483663-0.158637311586-0.1100138579740.123183015125-0.04387667265450.0250549798080.243353065832-0.0282628823264-0.2263090732920.03578075672330.300329297583-0.0366494344571-0.01437477249280.250307298430.0284338149570.30187532558315.6075806358.7607430455218.667677196
442.393095532311.368818699941.269832821471.239052486270.7388788873150.9230887673050.046946674879-0.309615100279-0.118611308995-0.0346224613369-0.03729279777540.0482064817511-0.000663211725082-0.1252753103870.006459493317530.318166120832-0.0185043836092-0.00557649074560.3092817079640.01830138327520.31410896959113.294105242852.9546991234213.614524501
452.146075455610.561085843601-0.6177376055481.07604698169-0.04114321325314.34313242987-0.0126580436034-0.149034876799-0.0666406813489-0.159246123044-0.0314148556079-0.03260998387820.08715551284980.1254648684340.0350717765070.349818720488-0.0307555737867-0.01593640624640.2665419847140.04240153826550.3633827282581.0621124435946.6486805285199.808122055
462.290474288870.163029171424-1.119790351431.942106801630.767576039621.89573541686-0.109043463458-0.1002019384-0.690604433873-0.484194065421-0.04128015086880.01619147180760.554030231795-0.1262128069730.1133845578550.510036297947-0.03330826028490.006266267517460.28239294880.04697799786910.515396585719-2.4821663536135.8479498699197.87272288
471.172034777650.7715224447221.257386993642.5356340211.166021773583.43137433792-0.1943289302710.5160835679150.198924146727-0.555821164369-0.0275928402520.26617618038-0.5293580154360.2781207347830.1646203410590.341211243283-0.0959760728324-0.0637368848530.4137421034970.06918488783660.30893577182628.519758055967.6412011734195.554955467
482.372672003460.5305588365160.8324115030751.981203785061.005524982121.70034425116-0.1141970994380.3539037696790.142747422907-0.08839826896830.0930839078154-0.0569234403416-0.1558097513930.227157402020.00825401859480.293558713477-0.0759927008765-0.008278585661660.3429689369720.05403719238120.26858438441534.962247055767.4298933807204.257310436
491.07605208186-0.171709729064-1.145905711482.10091993411-0.151223645261.29534225743-0.101379629611-0.05789371660430.1198416411580.2513607654320.03210513526760.0170873546782-0.1547193823270.233944487967-0.005208460883450.341843957611-0.0530158630888-0.05968516926170.3339035463530.04102162573240.38797535971129.313292825371.968660401215.253985194
502.830596735221.41552740941.875805334561.140453131420.5971328064722.754712185220.1274821347080.0720334031544-0.3040199422840.0878507610727-0.042404104013-0.1510155026160.1859955799960.737218255653-0.03779119124830.326684368995-0.00401439795152-0.0004183510163080.448278661661-0.000723326906230.33050527106525.483528614954.0268108189187.636858559
512.0671023067-0.166554516489-0.4041929368381.05303892512-0.9200730523451.309970955080.148227285678-0.05503539200080.0542558643908-0.00978787195719-0.04771487213570.0975868336609-0.1424962512920.0305446912587-0.08618433906830.343399503721-0.0519501173642.60701888436E-50.266470467605-0.00880428139230.3025188403151.3398616311453.8902101966193.552158816
522.532138316150.784398383539-0.6160927471521.20669997595-0.1465778122382.7943241850.239555362245-0.50052109086-0.011946599558-0.0114423235544-0.204966540355-0.326006365919-0.01263370337350.555435529035-0.02703859918490.403978794547-0.0605036238179-0.01786577896730.4116301610670.04725438257250.32401804600211.188998475852.3042030405195.741765678
531.987750472460.578818142692-0.9574935047330.5778437222680.02454128573960.7536394733620.1157032952620.1099582999510.389230356551-0.06597292571840.03563195358960.151794650272-0.311927275390.0306941793027-0.1464421771940.425980574463-0.04195202644670.009216500232610.2856779343150.04888979506610.354643839041-1.8179864949558.7809874479193.014200321
543.38416587638-0.628434316928-1.129547120061.34063013468-0.147954366572.120308919970.2797669568590.123540596015-0.01355800368290.0602899768635-0.114936447924-0.0233646675194-0.09875099780080.0256606052705-0.1306568538350.378276651047-0.0496117039843-0.04177064670610.3057419878840.04169677714320.27253623055814.46302688759.1169169528181.689587866
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 84 )AA0 - 841 - 85
22chain 'A' and (resid 85 through 158 )AA85 - 15886 - 159
33chain 'A' and (resid 159 through 205 )AA159 - 205160 - 201
44chain 'A' and (resid 206 through 270 )AA206 - 270202 - 266
55chain 'B' and (resid 0 through 11 )BE0 - 111 - 12
66chain 'B' and (resid 12 through 19 )BE12 - 1913 - 20
77chain 'B' and (resid 20 through 41 )BE20 - 4121 - 42
88chain 'B' and (resid 42 through 51 )BE42 - 5143 - 52
99chain 'B' and (resid 52 through 61 )BE52 - 6153 - 62
1010chain 'B' and (resid 62 through 71 )BE62 - 7163 - 72
1111chain 'B' and (resid 72 through 77 )BE72 - 7773 - 78
1212chain 'B' and (resid 78 through 83 )BE78 - 8379 - 84
1313chain 'B' and (resid 84 through 90 )BE84 - 9085 - 91
1414chain 'B' and (resid 91 through 97 )BE91 - 9792 - 98
1515chain 'C' and (resid 0 through 83 )CF0 - 831 - 84
1616chain 'C' and (resid 84 through 171 )CF84 - 17185 - 172
1717chain 'C' and (resid 172 through 237 )CF172 - 237173 - 238
1818chain 'C' and (resid 238 through 270 )CF238 - 270239 - 267
1919chain 'D' and (resid 1 through 17 )DH1 - 171 - 17
2020chain 'D' and (resid 18 through 52 )DH18 - 5218 - 52
2121chain 'D' and (resid 53 through 75 )DH53 - 7553 - 75
2222chain 'D' and (resid 76 through 108 )DH76 - 10876 - 108
2323chain 'D' and (resid 109 through 135 )DH109 - 135109 - 130
2424chain 'D' and (resid 136 through 150 )DH136 - 150131 - 145
2525chain 'D' and (resid 151 through 175 )DH151 - 175146 - 170
2626chain 'D' and (resid 176 through 184 )DH176 - 184171 - 179
2727chain 'D' and (resid 185 through 199 )DH185 - 199180 - 194
2828chain 'E' and (resid 3 through 94 )EI3 - 941 - 92
2929chain 'E' and (resid 95 through 109 )EI95 - 10993 - 107
3030chain 'E' and (resid 110 through 124 )EI110 - 124108 - 122
3131chain 'E' and (resid 125 through 140 )EI125 - 140123 - 138
3232chain 'E' and (resid 141 through 215 )EI141 - 215139 - 213
3333chain 'E' and (resid 216 through 244 )EI216 - 244214 - 242
3434chain 'F' and (resid 0 through 19 )FJ0 - 191 - 20
3535chain 'F' and (resid 20 through 30 )FJ20 - 3021 - 31
3636chain 'F' and (resid 31 through 41 )FJ31 - 4132 - 42
3737chain 'F' and (resid 42 through 56 )FJ42 - 5643 - 57
3838chain 'F' and (resid 57 through 71 )FJ57 - 7158 - 72
3939chain 'F' and (resid 72 through 90 )FJ72 - 9073 - 91
4040chain 'F' and (resid 91 through 99 )FJ91 - 9992 - 100
4141chain 'G' and (resid 1 through 52 )GM1 - 521 - 52
4242chain 'G' and (resid 53 through 75 )GM53 - 7553 - 75
4343chain 'G' and (resid 76 through 91 )GM76 - 9176 - 91
4444chain 'G' and (resid 92 through 120 )GM92 - 12092 - 120
4545chain 'G' and (resid 121 through 175 )GM121 - 175121 - 175
4646chain 'G' and (resid 176 through 200 )GM176 - 200176 - 200
4747chain 'H' and (resid 1 through 25 )HN1 - 251 - 25
4848chain 'H' and (resid 26 through 94 )HN26 - 9426 - 94
4949chain 'H' and (resid 95 through 109 )HN95 - 10995 - 109
5050chain 'H' and (resid 110 through 124 )HN110 - 124110 - 124
5151chain 'H' and (resid 125 through 162 )HN125 - 162125 - 162
5252chain 'H' and (resid 163 through 188 )HN163 - 188163 - 188
5353chain 'H' and (resid 189 through 215 )HN189 - 215189 - 215
5454chain 'H' and (resid 216 through 245 )HN216 - 245216 - 245

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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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