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- PDB-9bu0: Structure of human MAIT A-F7 TCR in complex with human MR1-salicy... -

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基本情報

登録情報
データベース: PDB / ID: 9bu0
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-salicylaldehyde
要素
  • Beta-2-microglobulin
  • Human TCR TRAV1-2_ALPHA
  • Human TCR TRBV6-1_BETA
  • Major histocompatibility complex class I-related gene protein
キーワードIMMUNE SYSTEM / antigen presentation / MAIT cells / T cell receptor / MR1
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 / phagocytic vesicle membrane / recycling endosome 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
ACETATE ION / SALICYLALDEHYDE / 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: 2.89 Å
データ登録者Awad, W. / Rossjohn, J.
資金援助 オーストラリア, 2件
組織認可番号
Australian Research Council (ARC)DE220101491 オーストラリア
National Health and Medical Research Council (NHMRC, Australia) オーストラリア
引用ジャーナル: J.Exp.Med. / : 2025
タイトル: Cigarette smoke components modulate the MR1-MAIT axis.
著者: Awad, W. / Mayall, J.R. / Xu, W. / Johansen, M.D. / Patton, T. / Lim, X.Y. / Galvao, I. / Howson, L.J. / Brown, A.C. / Haw, T.J. / Donovan, C. / Das, S. / Albers, G.J. / Pai, T.Y. / Hortle, E. ...著者: Awad, W. / Mayall, J.R. / Xu, W. / Johansen, M.D. / Patton, T. / Lim, X.Y. / Galvao, I. / Howson, L.J. / Brown, A.C. / Haw, T.J. / Donovan, C. / Das, S. / Albers, G.J. / Pai, T.Y. / Hortle, E. / Gillis, C.M. / Hansbro, N.G. / Horvat, J.C. / Liu, L. / Mak, J.Y.W. / McCluskey, J. / Fairlie, D.P. / Corbett, A.J. / Hansbro, P.M. / Rossjohn, J.
履歴
登録2024年5月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年12月25日Provider: repository / タイプ: Initial release
改定 1.12025年1月29日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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


分子量 (理論値)分子数
合計 (水以外)188,86416
ポリマ-188,1008
非ポリマー7648
2,018112
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
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)217.092, 71.188, 144.387
Angle α, β, γ (deg.)90.000, 104.760, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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 Human TCR TRAV1-2_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 Human TCR TRBV6-1_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 , 4種, 120分子

#5: 化合物 ChemComp-NK / SALICYLALDEHYDE / サリチルアルデヒド


分子量: 122.121 Da / 分子数: 2 / 由来タイプ: 合成 / : C7H6O2 / 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: 5 / 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: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 112 / 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: 2.97 Å3/Da / 溶媒含有率: 58.64 %
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: PEG 3350, Na 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: MX2 / 波長: 0.9322 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年10月10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: 0.9322 Å / 相対比: 1
反射解像度: 2.89→48.27 Å / Num. obs: 148434 / % possible obs: 98.1 % / 冗長度: 3.1 % / Biso Wilson estimate: 40.35 Å2 / CC1/2: 0.879 / Net I/σ(I): 10.47
反射 シェル解像度: 2.89→2.993 Å / Num. unique obs: 14575 / CC1/2: 0.866

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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
XDS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: 2.89→34.99 Å / SU ML: 0.3545 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 22.723
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2377 3488 4.24 %
Rwork0.2031 78765 -
obs0.2045 82253 87.9 %
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: 38.52 Å2
精密化ステップサイクル: LAST / 解像度: 2.89→34.99 Å
タンパク質核酸リガンド溶媒全体
原子数12332 0 50 112 12494
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.008912856
X-RAY DIFFRACTIONf_angle_d1.065617529
X-RAY DIFFRACTIONf_chiral_restr0.05431887
X-RAY DIFFRACTIONf_plane_restr0.00972282
X-RAY DIFFRACTIONf_dihedral_angle_d22.52224539
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.930.3231410.24583115X-RAY DIFFRACTION86.16
2.93-2.970.2761280.24163053X-RAY DIFFRACTION85.37
2.97-3.020.3031350.24443085X-RAY DIFFRACTION86.05
3.02-3.060.27861370.24522999X-RAY DIFFRACTION84.62
3.06-3.110.35131310.24512957X-RAY DIFFRACTION82
3.11-3.170.36611330.24793064X-RAY DIFFRACTION84.38
3.17-3.220.28471350.24123086X-RAY DIFFRACTION86.31
3.22-3.290.24791350.22673112X-RAY DIFFRACTION87.99
3.29-3.350.27571390.2173133X-RAY DIFFRACTION86.15
3.35-3.430.28941350.21692966X-RAY DIFFRACTION84.04
3.43-3.510.25161460.21453149X-RAY DIFFRACTION87.94
3.51-3.590.30171440.21953223X-RAY DIFFRACTION89.81
3.59-3.690.27771460.20783234X-RAY DIFFRACTION90.71
3.69-3.80.20161370.21173279X-RAY DIFFRACTION90.11
3.8-3.920.20471460.19843212X-RAY DIFFRACTION89.88
3.92-4.060.25011400.19673232X-RAY DIFFRACTION90.91
4.06-4.220.23861500.19313246X-RAY DIFFRACTION89.7
4.22-4.420.20481440.16853229X-RAY DIFFRACTION90.57
4.42-4.650.18071340.16393219X-RAY DIFFRACTION90.3
4.65-4.940.17161420.17023211X-RAY DIFFRACTION89.58
4.94-5.320.19011440.17993190X-RAY DIFFRACTION89.5
5.32-5.850.24471360.19653112X-RAY DIFFRACTION86.02
5.85-6.690.23781410.21293192X-RAY DIFFRACTION89.21
6.69-8.410.20921450.19483225X-RAY DIFFRACTION89.99
8.41-34.990.18051440.19093242X-RAY DIFFRACTION90.32
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)
11.38473245675-0.8794595442380.331907305071.654462489460.8088868004240.929305557240.03661041200670.07066659811180.154282234954-0.2101334121450.0130750797283-0.0960655041443-0.0951207378876-0.0151895325117-0.05392184229810.238344256045-0.0457955031601-0.009295963203450.2584395349270.06512898179930.31442438871748.27747734178.7536404882225.161867482
21.614373948620.3620339216780.238071912281.114037083090.2490443123860.2379624967280.07981484514410.326844292962-0.02262838051120.04560811367180.04637663592920.1273865753860.08397143854880.142498803366-0.09370290633990.2044642230040.0284228344389-0.006578428444210.343049045782-0.02893835694570.17218493885740.385333784377.6871719644236.40048717
31.18590750754-0.1417247908810.2758726553430.7741212111810.2074125095721.77588854574-0.170744627824-0.2026227305290.4496078996850.2081950955430.05777232553550.044637778766-0.400583778976-0.05563531942320.1622433050790.3472172933510.0924026184887-0.05085193860640.388098829373-0.09648823861070.45646723813167.345832683681.9457828276256.824974918
42.77077894739-0.7045062373910.1215297581741.92918977297-0.09225353317891.037617433790.04251321394250.05421070855260.767993771298-0.03616934892280.05619000716680.028688405590.220033125436-0.0307955280073-0.1324443271980.359438939583-0.0688347867647-0.1149720672610.2210393959330.009594332296180.63320202765362.157315546993.0005065585239.812662963
50.11305506420.153017598151-0.3456027237081.07803388486-0.07202790190281.14718030842-0.1215557600460.09525829072510.1491301260370.09244947462310.08572902529-0.716556119996-0.1543081592340.5917475401240.1249723308750.282391510778-0.0798735179151-0.04016696577160.5051179208680.02774087522350.69443794651773.092401629685.1168273195238.938423917
61.99993840836-1.49533199948-3.103160815670.1537938195190.315660645290.656020914267-0.2777712150740.6857072004610.465558925792-0.307923079989-0.30755845284-0.00897875851973-0.1554269367390.3069890083710.4579934275970.291648333857-0.07909454473460.1229368488720.68842305449-0.02650510119990.80181612710754.503228047694.0626364749230.243865284
71.49873110071-1.211250883151.152817945460.939356826091-0.9068851589310.8547185825770.04159022579220.01940688629840.37222323251-0.287416026059-0.346940448052-0.74304049579-0.2336869842950.2789407031090.2730391606030.387421783307-0.0202131765697-0.04941292547440.48063403246-0.09921932935060.81125535690374.130572725994.7014717085229.558039851
85.777378334623.133897750340.223309390821.686336632840.115344033495-0.00110528350066-0.0053309380720.2726919637960.033330607655-0.1601563042310.0375376722453-0.0518359010797-0.08137753621660.31854138091-0.04469902619740.259463771077-0.0361186679214-0.1187820099120.922606864186-0.2977893865960.50722580399766.665733899584.353819937227.826751294
92.910671560710.866720705046-0.535326358560.430285313275-0.2509221833190.136996006595-0.4744781837330.458284075064-0.128135885266-0.3287955248290.292167042518-0.2164101289750.1025485976860.3169539462180.2299806274890.3013006092290.001255057186020.09957512839070.316781117775-0.05395827584040.27688441054951.231179479785.7398788291235.845279801
105.22771770261-0.724962088167-1.683796154211.80391305719-0.3301308338451.46621755529-0.02210296490630.2828344385370.276375441677-0.0761229770435-0.071724579188-0.449143391720.3052359908490.11046312220.1542169718930.273247265636-0.0346870468836-0.04556601582580.3346793875010.002593164093250.36191222663468.95266761785.7339314763233.32015743
111.3559573244-1.353966938740.2078551491081.31275848455-0.3417175716920.7797893450190.0713312693617-0.5404789699760.2670182571550.44018070881-0.13588338018-0.433811795796-0.4322772273370.185940852540.1551912854310.471216510131-0.293354910545-0.1501990608810.5989784012920.07473722928640.82229181664176.411255177894.9229136209235.616311177
122.56433611175-0.732755362599-1.044472043831.160155222460.4651980219780.4445049836970.2316998270340.1865725335180.3737066526960.295242054901-0.2256201726760.0427172228444-0.352517452765-0.1186957890560.181134123570.38388999833-0.0501509323907-0.2181785498430.680657186654-0.1432279674640.78360052706766.490882652599.2336846249237.022114272
130.62471911740.233831953474-0.3168910040381.980169282940.1363898947360.6347975793080.01079855639720.105862270828-0.02178144613970.0846402549659-0.02281998363840.2596059887740.007423030111060.04186720597080.011244073720.2423117227910.02333835763420.008170900199660.260947917799-0.03669756089720.255633774786-6.6429515002264.0350915533161.383260608
141.73019840118-0.295075618189-0.2601728805621.8761699428-0.5195629073521.14548753647-0.101857815786-0.1518547203140.03341852175760.2421967001940.0334775375229-0.09977729099760.1075830706110.144792641270.03556886977940.257335537793-0.03282078640060.01237324482760.297689203754-0.01779277669180.1633204416271.4718135233257.3682055092171.889378169
151.902135938850.824533809040.5125801762291.26546199056-0.3138290799640.639065729729-0.04210154177350.145767471526-0.04625777320130.190002966094-0.03437399915120.151395849140.03879520979880.002519647939490.1307445853620.3163617621320.07436386008670.05034177601210.224751969962-0.02383343523890.334669275878-22.395578418773.8831988401192.348882694
162.98308731706-0.09329004463420.03960389727910.2665331972730.09239600909751.14438285176-0.0535867472294-0.460526780827-0.1687305378180.0410063229732-0.0336247749846-0.05473732617550.0653285826205-0.04202058891150.0724077673220.284557438676-0.0533229769853-0.006826712198520.2743512153110.08646111276290.20828088530126.540779859864.3024543623160.927330997
172.90231219301-0.317521777623-1.984072568870.3666563324280.6885007668411.927429071510.0476589826492-0.65032155109-0.0304344200349-0.1174218205350.260860971218-0.096583029343-0.1408516359580.918979695657-0.2550403038690.3873212953950.068030199323-0.005605245837330.41202728278-0.04977623222910.35335592455952.411314591364.2792297156143.516503293
181.84445268696-0.588525510.7157525362561.241703599041.010923698991.890303242760.2009978715810.2100173074230.1981757841730.1367520538680.468887777172-0.544417883808-0.04766999699520.311515820228-0.6545990303810.378494085845-0.03365301895190.03057008026940.5556085639940.08009998802570.60608621378854.275736688263.9346480483140.435905989
190.3597514579140.143721691053-0.2647720955261.08249446599-0.171671996720.2012494333960.0567627756280.566689809597-0.0177244641017-0.389303612379-0.369754162850.038003742410.242993904428-0.05562875548040.3522008658150.3638401687430.04912414599960.01455182491710.7019628370950.04534837907990.24925429490218.692138048963.325632117131.398484176
201.983829996510.381205580054-1.030262010234.50678087439-3.107057322025.64467980338-0.1531526633160.0752763084668-0.0414731820024-0.464496662878-0.1455910452710.1068686520550.3431159279520.1377638317990.1852260097670.353105562079-0.07068947995030.0117022773410.309297310265-0.02640565991750.20261650407810.766600273855.4026539165142.324465899
212.239755820680.401047607204-0.3358989299281.97102889339-0.08736624026441.3522105160.126353765291-0.6977342403560.288158550572-0.251102609591-0.4336345651940.0141229864024-0.04833870434360.5709983698780.2726105972670.274011605406-0.0252248448717-0.03653471436970.496278592712-0.004806710907230.18382395997411.947042210667.8703346153145.853575146
222.133776514040.79557049305-0.8546781156622.86233124763-1.321927177582.27897291283-0.3596232124570.594870212895-0.250979500007-0.8712473909320.405200127151-0.2663064620170.620207255118-0.216721278548-0.07891672766240.314311435687-0.06665363734380.003955511346160.376768676797-0.06583802968330.2046190552867.8461413430463.2816145321137.702877812
230.95264809737-0.3024781635790.6165023718272.87333001305-0.2716165316721.97319086819-0.327833544138-0.04733137007750.2374320577260.3359684290270.1400705236310.00764761390742-0.2454613804380.05741708138960.2006081794540.232917444524-0.0371544141691-0.007799678700470.5262726216640.01400779533480.26373707776715.652760884961.4834333884147.912384666
242.95429706448-0.212163580968-0.8713252333911.013058630071.222469765311.722977948860.377795545032-0.0364686624580.1295975166470.3452079842750.427392795417-0.1428260368960.2261545091560.151814575233-0.619976722870.327970667072-0.09226859335920.02403308400850.5796061205180.1116924014390.31665917544927.38871446868.5082052555126.378371748
251.233062777940.700561372227-0.3911503467231.534646554810.6326879549560.7476059519840.1177060054750.0803623068519-0.0389650712216-0.332981608410.0108419663388-0.3225229716970.3473115540860.409654526435-0.1454064406180.5010710163550.1136848341420.004909434671680.7381306798980.1122201704580.51936958088456.163847221454.7506519972133.605124333
262.93710905320.950340468718-0.04775655018940.87268652620.1709140572611.665048033050.382344005379-0.453070224498-0.088067429258-0.132762698287-0.146748565746-0.007841560841460.2850917910820.621227686394-0.2349209767710.3842894840770.04405739549960.03303920293610.451669060939-0.03759964713940.22852298964240.363807085958.2671010307131.883019523
270.682479504711-0.1025193555810.2907263879142.53033846503-0.3755656077491.606729551810.02980315630750.0872975675764-0.186412795879-0.08506805335710.2340073747130.4371520737780.522477420663-0.0319470415809-0.2474530504860.3966856648510.03413953226210.01228325692610.240029257141-0.04048753209440.34249220311539.641958979564.48722467133.803235884
280.6539494215420.262134411006-0.8126449392162.6543172568-0.02107426839561.657207426680.3536732326020.646215119671-0.2874016431510.4178022985010.0917646387536-0.3528510569581.213419370250.409787395665-0.3951509241340.5719503092770.10977456927-0.1608433515430.615389957028-0.1039418153880.35708143574246.344325723452.4821358316134.006376777
292.72294102488-0.593848460451-1.417310829943.82767767203-1.870832178553.652158800870.2497197127790.343259444922-0.235346041533-0.4942188800611.023214781920.3417663932520.220675077702-0.420608910851-1.084181698190.576491100305-0.0226420422539-0.0940613845960.325778922309-0.0292062600730.49523667644930.025100582760.4385394792120.038759985
302.94243959073-0.7125009899870.5703664224993.78130471542-0.6011218958042.47330648916-0.1430558413760.287026356167-0.2954003691260.160427648903-0.0994546425425-0.195324815254-0.0179574789368-0.03785305442950.2278092903370.1724685705740.005408521809570.02691722493290.3788013635550.0772348570760.28405570629-25.555912673359.7806136043175.63673302
310.968081588519-0.02218511711180.4769508756230.5875731196260.02344976439121.3450092383-0.1510513096530.2938071204370.2718704773780.205768795414-0.0668019646890.58249672105-0.1649033920760.01481211311670.1751582107730.3948069203890.0156786519379-0.0538512943380.196281312782-0.009525754856290.463253778014-30.279386020574.2576970141176.595726766
323.30037644748-0.525831102587-0.7555230806660.8469291692590.4558185231610.6515584013210.1239529233230.2604545035020.210063569525-0.344279179464-0.06769229521730.155084475128-0.140894347832-0.0317302473708-0.04295807241310.3339239044850.0113932439985-0.02297828935690.330987830645-0.05270544806790.309555067795-28.229533291566.1549219492166.010053268
334.15144367768-2.0484613837-0.8851619889512.078614750650.6404973407610.7638939120050.2061248263170.2341018283270.197743428786-0.237321982432-0.1989007164440.183139053716-0.0780209301257-0.1709129462190.04630261731770.371984358520.0452490775976-0.01178432670280.2518815807150.03831143008360.351756140398-27.796349300169.1064889225172.624010204
342.05391689159-2.48965773682-1.318953141834.061868652150.351524217752.40341276050.006904613526620.4522964107540.217843384424-0.503376171482-0.3859513193230.3854497771750.212274858043-0.2963384378840.325057251090.2307997376510.0714544437902-0.09769835155250.543658534967-0.1316602075090.455530548064-32.907221392457.9720164566169.058440469
351.735841824260.2179804260411.216148955384.610790471140.8809417637550.9813988509290.150314991976-0.4117892911430.187466674060.73644313966-0.008479744899351.0531905013-0.6482899706310.0329639965406-0.06401895395320.524494072169-0.09846758137330.2034419056690.255776247648-0.09751200682350.472491311089-36.917213475967.4743184805179.474361422
361.440631121410.7643997726760.1976267944872.855767522260.3551723763391.9877474985-0.134012492081-0.391444500909-0.1986069989030.150470060716-0.0821719656127-0.249269079908-0.334406355754-0.2102290733220.172962372010.2301465062450.06483317353610.009146656364930.4264677561860.09175580350.11331644203518.862962191351.3400305559221.520458511
370.1283963948140.1627240249160.1260867117811.31967932506-0.6064704011431.40490851514-0.07489314934420.763809973106-0.271909548625-0.05061715870820.376195520393-0.1369273994140.144273637925-0.103922022009-0.2015065207760.242414314242-0.0324519752263-0.0827893792690.35154910049-0.08140903573320.35596477465425.73680625758.6660663349224.808921014
382.294640525090.00703768598827-1.201961950490.788392822745-0.03636870160580.6482492239920.02407172394760.3749544765840.6368407178120.209717586282-0.24921302901-0.0777443417158-0.180569347165-0.5037911767280.1798240639330.229429887055-0.06048989702020.00696751824430.1740987077540.09409507830260.41847993040419.468559081164.9038088379217.964583158
392.957665028920.8192434424121.428703808552.297043329370.6565976704652.930739062940.197552767114-0.157785990101-0.08371500544410.4204710292070.089818183350.1852587740990.104111036425-0.142014729768-0.2673388291450.342903387669-0.03414993381560.02920846295440.337160876391-0.0248331888630.28669391269820.680091413261.9909080251232.678172327
401.65037530198-0.120226809051.365746908061.026283197840.05214479544992.336700217340.0143947421607-0.453716070732-0.4583269389680.139619574196-0.04270127949590.107968600789-0.204101250855-0.4911865511840.002238935172040.323574455455-0.0279296270408-0.05641335123090.3735621226110.054647369880.24544623243412.182181406257.8497106961224.476508336
411.401833912870.5545130523830.5068110880140.614417802768-0.06364641317060.9762796378420.0893153893687-0.022538734932-0.0525301309476-0.00340297638628-0.086945724938-0.0505462615810.0742972678626-0.0296555020634-0.01691308093690.2418575821630.01781427347180.05555609961370.3081205099630.02075194525980.2069257200679.7938084541552.5019133229209.1601968
422.300290962480.09144975055580.6812254025472.84205309988-0.03117851903282.886991528930.3211172417920.550881802592-0.4446552324080.351518461585-0.54460411874-0.3124466230490.7061935316310.6159152504020.1846888707470.4568581417460.1103413330450.04253476406750.6255410979260.2055360243940.4622552468383.2463039372240.1190567326205.574703761
433.44221263446-0.7736133677230.2322711805724.62542831541.204217049734.13229181552-0.04820704800450.201291012430.6443559832520.4445839599090.07422903779580.0981921941889-0.1762684838250.507697320637-0.08623924867070.218735828602-0.142784961036-0.002654842248260.3373876910670.14005185310.3422706940450.15364878726352.3747837181206.081201465
441.731103303930.227534138518-0.7410549500770.420088910884-0.4688962332590.723249264008-0.5762327713830.156352164928-0.466343803239-0.04179573128530.008116655590820.7551427681960.6818215483730.003654201552510.5035731127970.54671879568-0.09205584492640.06103694980590.2611956138210.03719193057680.402416266685-0.84850849543842.7497989494198.071444509
452.05211747386-0.573431013601-1.119067171443.80798971057-0.7166736808243.706332820350.93147819538-0.06080942436120.0630633351193-0.2348176998610.1793450291280.5806977912750.4035264893810.338333089972-0.8403843357680.4145462809440.03119910441890.04620084904880.2396146864840.04472391458940.377407090778-6.6059342230736.7994970116204.402336358
461.405125286260.9843456930041.358894879181.636806400180.0815005907181.91677766304-0.2785285990320.2889226183380.527267601409-0.21221583963-0.174907715028-0.0149173779992-0.371804860634-0.05088039091170.4511213153630.425897396004-0.0901570265678-0.1123440331490.6229113231650.103457130710.084739318696824.632228236966.9193173894197.419709104
470.7747856692770.149811920106-0.4314771402171.851857051520.4514435799480.745246288013-0.02242201921030.07826063143020.00590230978124-0.2104282148490.007188380842850.164906298969-0.0247276508907-0.07507761325380.00707669113610.22407792181-0.0275661072771-0.02137759259440.3878078295450.0237389347580.20290785139831.404869448167.162412306206.13507423
480.478054970128-0.746736951414-0.2041990061071.80259698943-0.380177513531.37512694964-0.1882122818190.03767430725680.364150660694-0.1340877438970.319439302168-0.317438098304-0.03534385763120.339137849165-0.07966909151720.390711556031-0.1230258693610.0239767764250.2342689479250.002059457796660.38639149211538.108203071671.9413977304206.348833906
491.391021710270.0129760444834-0.4694661553861.965159267240.9949873588681.29917603979-0.09567612581930.226323441692-0.0482208221564-0.2059564564330.106965516931-0.165532894746-0.176970874316-0.0492268511410.07005621797970.300908638121-0.121451363805-0.1185386769250.4984899797880.06413932324490.29334818511432.314464295363.9502324236201.268541014
502.782457635781.11308910445-0.0007129962670493.091704859830.4492878814612.60662335314-0.1441468320850.30312001402-0.04320508768060.6496665123160.293868376883-0.0579437039478-0.4771967851650.612623520125-0.0772275014680.3538926476110.0297261942956-0.05749654726920.2648201711430.1235368430980.29910691733428.240686879472.56697924217.403900135
511.667287911320.4937814480141.537539668720.7778011199770.4211801435971.344769894050.4128754889360.154256018006-0.3183544407240.3367103880820.151742849985-0.4495122353030.7373055434370.21787599529-0.4058491569560.5316626272020.0809324885573-0.002783651516780.1887308934530.01059270334470.29905153610924.197477221454.6040408027189.503754779
522.779664286890.0335265337039-1.424590916231.48916887133-0.05179838512321.270656144420.134670297083-0.3308865923820.1782793384070.2409086284880.03111017295370.1502529006160.0153630555170.416361613128-0.0949377530820.308650711551-0.0834829700504-0.006350574191820.3158886374670.02497114389150.177654450020.22983068622354.4512406304195.509171854
533.19765353458-0.0800048356568-0.8290385264910.8169870042040.292166037682.370677938960.139784432869-0.6143306219-0.123269189656-0.5069074856570.0929003999076-0.240000156688-0.05474523042930.224385059244-0.2005053614350.380132860341-0.0606530298473-0.02657312008740.2664285297960.01836276286310.24341403020310.510253019152.8714001614197.254931803
541.78281447272-0.470229482433-0.4039733868260.4704076687240.1663406905870.5714053923020.0376032439058-0.1811343682480.0781023979096-0.245823303088-0.001468907269660.232271886002-0.101137944466-0.00311543729381-0.03873314584190.3344805264040.0821010576133-0.004317559410290.346779358896-0.03716191121780.268216220018-4.1370850195460.3728988706195.079280156
555.72817688583-1.41809921278-1.725765566110.846369337314-0.1513697055812.630203503430.4962710702620.293629440921-0.335911171869-0.112716934238-0.3070803468460.038377263971-0.1204418297040.249332508133-0.170880278220.36415664811-0.021661773965-0.06676164659040.2242563629430.01103034825770.19951976333412.947279050859.8171605871183.62277355
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 182 )AA85 - 18286 - 183
33chain 'A' and (resid 183 through 269 )AA183 - 269184 - 262
44chain 'B' and (resid 2 through 11 )BE2 - 111 - 10
55chain 'B' and (resid 12 through 30 )BE12 - 3011 - 29
66chain 'B' and (resid 31 through 35 )BE31 - 3530 - 34
77chain 'B' and (resid 36 through 48 )BE36 - 4835 - 47
88chain 'B' and (resid 49 through 53 )BE49 - 5348 - 52
99chain 'B' and (resid 54 through 61 )BE54 - 6153 - 60
1010chain 'B' and (resid 62 through 71 )BE62 - 7161 - 70
1111chain 'B' and (resid 72 through 83 )BE72 - 8371 - 79
1212chain 'B' and (resid 84 through 97 )BE84 - 9780 - 93
1313chain 'C' and (resid 1 through 84 )CF1 - 841 - 84
1414chain 'C' and (resid 85 through 171 )CF85 - 17185 - 171
1515chain 'C' and (resid 172 through 270 )CF172 - 270172 - 263
1616chain 'D' and (resid 1 through 102 )DJ1 - 1021 - 102
1717chain 'D' and (resid 103 through 150 )DJ103 - 150103 - 143
1818chain 'D' and (resid 151 through 198 )DJ151 - 198144 - 188
1919chain 'E' and (resid 4 through 18 )EK4 - 181 - 15
2020chain 'E' and (resid 19 through 30 )EK19 - 3016 - 27
2121chain 'E' and (resid 31 through 63 )EK31 - 6328 - 60
2222chain 'E' and (resid 64 through 82 )EK64 - 8261 - 79
2323chain 'E' and (resid 83 through 109 )EK83 - 10980 - 106
2424chain 'E' and (resid 110 through 124 )EK110 - 124107 - 121
2525chain 'E' and (resid 125 through 140 )EK125 - 140122 - 137
2626chain 'E' and (resid 141 through 162 )EK141 - 162138 - 159
2727chain 'E' and (resid 163 through 190 )EK163 - 190160 - 187
2828chain 'E' and (resid 191 through 215 )EK191 - 215188 - 206
2929chain 'E' and (resid 216 through 241 )EK216 - 241207 - 232
3030chain 'F' and (resid 1 through 11 )FL1 - 111 - 11
3131chain 'F' and (resid 12 through 30 )FL12 - 3012 - 30
3232chain 'F' and (resid 31 through 56 )FL31 - 5631 - 56
3333chain 'F' and (resid 57 through 77 )FL57 - 7757 - 77
3434chain 'F' and (resid 78 through 90 )FL78 - 9078 - 90
3535chain 'F' and (resid 91 through 99 )FL91 - 9991 - 99
3636chain 'G' and (resid 1 through 17 )GO1 - 171 - 17
3737chain 'G' and (resid 18 through 37 )GO18 - 3718 - 37
3838chain 'G' and (resid 38 through 49 )GO38 - 4938 - 49
3939chain 'G' and (resid 50 through 68 )GO50 - 6850 - 68
4040chain 'G' and (resid 69 through 84 )GO69 - 8469 - 84
4141chain 'G' and (resid 85 through 135 )GO85 - 13585 - 135
4242chain 'G' and (resid 136 through 150 )GO136 - 150136 - 150
4343chain 'G' and (resid 151 through 165 )GO151 - 165151 - 165
4444chain 'G' and (resid 166 through 185 )GO166 - 185166 - 185
4545chain 'G' and (resid 186 through 200 )GO186 - 200186 - 200
4646chain 'H' and (resid 2 through 14 )HP2 - 141 - 13
4747chain 'H' and (resid 15 through 49 )HP15 - 4914 - 48
4848chain 'H' and (resid 50 through 73 )HP50 - 7349 - 72
4949chain 'H' and (resid 74 through 94 )HP74 - 9473 - 93
5050chain 'H' and (resid 95 through 109 )HP95 - 10994 - 108
5151chain 'H' and (resid 110 through 124 )HP110 - 124109 - 123
5252chain 'H' and (resid 125 through 162 )HP125 - 162124 - 161
5353chain 'H' and (resid 163 through 190 )HP163 - 190162 - 189
5454chain 'H' and (resid 191 through 215 )HP191 - 215190 - 214
5555chain 'H' and (resid 216 through 245 )HP216 - 245215 - 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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