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- PDB-9o07: Structure of human MAIT A-F7 TCR in complex with human MR1-lumiflavin -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 9o07
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-lumiflavin
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha
  • TCR-beta
キーワードIMMUNE SYSTEM / receptor
機能・相同性
機能・相同性情報


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / 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
LUMIFLAVIN / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.97 Å
データ登録者Abdelaal, M. / Rossjohn, J. / Awad, W.
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: To Be Published
タイトル: Major histocompatibility complex class I-related gene protein / TCR alpha /TCR beta / Beta-2-microglobulin complex
著者: Abdelaal, M. / Rossjohn, J. / Awad, W.
履歴
登録2025年4月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年11月19日Provider: repository / タイプ: Initial release

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


分子量 (理論値)分子数
合計 (水以外)188,72812
ポリマ－188,1008
非ポリマー6284
水25,3831409
1
C: Major histocompatibility complex class I-related gene protein
D: TCR-alpha
E: TCR-beta
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,3296
ポリマ－94,0504
非ポリマー2792
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Major histocompatibility complex class I-related gene protein
B: TCR-alpha
G: TCR-beta
H: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,3986
ポリマ－94,0504
非ポリマー3482
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)212.712, 69.293, 141.169
Angle α, β, γ (deg.)90.000, 103.481, 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 CADBEGFH

#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 TCR-alpha


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


分子量: 27677.760 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#4: 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

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非ポリマー , 4種, 1413分子

#5: 化合物 ChemComp-LFN / LUMIFLAVIN / 7,8,10-TRIMETHYLBENZO[G]PTERIDINE-2,4(3H,10H)-DIONE


分子量: 256.260 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C13H12N4O2 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-NA / SODIUM ION


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1409 / 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: 2.69 Å3/Da / 溶媒含有率: 54.26 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.3 / 詳細: Bis-Tris-propane, PEG3350 and sodium 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: 0.953739 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年12月3日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.953739 Å / 相対比: 1
反射解像度: 1.97→49.32 Å / Num. obs: 141041 / % possible obs: 99.66 % / 冗長度: 2 % / Biso Wilson estimate: 37.75 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.03
反射 シェル解像度: 1.97→1.99 Å / Num. unique obs: 4650 / CC1/2: 0.618

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207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 / 解像度: 1.97→49.32 Å / SU ML: 0.209 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 20.1257
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.1945 7154 5.07 %
Rwork0.157 133873 -
obs0.1589 141027 99.66 %
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: 43.75 Å2
精密化ステップサイクル: LAST / 解像度: 1.97→49.32 Å
タンパク質核酸リガンド溶媒全体
原子数12689 0 45 1410 14144
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006813499
X-RAY DIFFRACTIONf_angle_d0.844518476
X-RAY DIFFRACTIONf_chiral_restr0.05541983
X-RAY DIFFRACTIONf_plane_restr0.00712435
X-RAY DIFFRACTIONf_dihedral_angle_d13.38584924
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.26652220.24284428X-RAY DIFFRACTION99.51
1.99-2.020.27892440.2394395X-RAY DIFFRACTION99.49
2.02-2.040.26282360.22384487X-RAY DIFFRACTION99.58
2.04-2.070.28192450.21914373X-RAY DIFFRACTION99.55
2.07-2.090.23922470.21194432X-RAY DIFFRACTION99.53
2.09-2.120.24322200.20324429X-RAY DIFFRACTION99.68
2.12-2.150.24892460.19434502X-RAY DIFFRACTION99.77
2.15-2.180.2422440.18994399X-RAY DIFFRACTION99.74
2.18-2.220.24052260.18654434X-RAY DIFFRACTION99.76
2.22-2.260.24882210.184478X-RAY DIFFRACTION99.85
2.26-2.290.26232140.18954438X-RAY DIFFRACTION99.96
2.29-2.340.2272640.18444459X-RAY DIFFRACTION99.92
2.34-2.380.24642260.17554502X-RAY DIFFRACTION99.87
2.38-2.430.19942120.17174434X-RAY DIFFRACTION99.79
2.43-2.480.22722420.17614486X-RAY DIFFRACTION99.83
2.48-2.540.21472250.17534454X-RAY DIFFRACTION99.85
2.54-2.60.2412670.17664427X-RAY DIFFRACTION99.87
2.6-2.670.23522590.18244466X-RAY DIFFRACTION99.81
2.67-2.750.23962470.18614431X-RAY DIFFRACTION99.74
2.75-2.840.22392650.18364408X-RAY DIFFRACTION99.79
2.84-2.940.22012390.16934477X-RAY DIFFRACTION99.66
2.94-3.060.21642600.16154422X-RAY DIFFRACTION99.53
3.06-3.20.21492380.15594470X-RAY DIFFRACTION99.39
3.2-3.370.18552500.15674443X-RAY DIFFRACTION99.53
3.37-3.580.17192380.13914485X-RAY DIFFRACTION99.6
3.58-3.860.15412230.13034512X-RAY DIFFRACTION99.66
3.86-4.240.1532190.12364522X-RAY DIFFRACTION99.66
4.24-4.860.13942480.11264508X-RAY DIFFRACTION99.73
4.86-6.120.16972370.13974536X-RAY DIFFRACTION99.65
6.12-49.320.18692300.17144636X-RAY DIFFRACTION98.7
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)
12.580929068040.2754144265910.3190141558082.771284350720.05116359651182.800255808470.1483839973840.162779464771-0.0368594396547-0.0503753772989-0.05363598849330.2149277785590.0830978118898-0.0314042848666-0.08550576300430.207976614944-0.004251456882190.006495149630720.207520977924-0.009556559004670.20838196614230.2651360733-5.7157904417220.7830402727
22.58743806899-0.5960023859950.09296111646352.92145140361-1.690818648962.052810923470.188025686978-0.053456910931-0.1863514936550.28380848773-0.154376033111-0.1078130050930.1359603214530.13820405209-0.02501232951030.27209796261-0.0368203357911-0.00566466038730.230519952648-0.01299510241790.1671446037638.1686762728-13.56985142331.3515552492
32.306656441250.612437283383-0.3409804852272.375774007920.4845874708572.11331969855-0.00572176749205-0.18617426398-0.198474509787-0.00606425868207-0.01965431629790.1757494768720.155952324033-0.1236266915660.03739714461530.2676904670380.002503090832650.03540152619310.199924563515-0.005371000668140.31955789664315.18627219672.7431133182750.3249392065
42.210467703940.4574339457231.238013981283.569245358530.148744091623.521073265390.0931162603982-0.293906938273-0.1449411738380.344865625514-0.01808134777280.3360446743220.186702482194-0.48496554176-0.1030601577790.253270719548-0.01557511511770.08183506720380.2490128315680.01466610743960.33325865498715.36193224013.864190378656.6297422852
55.89158795372-2.633688579370.08383080501094.084927547-0.8915549057851.52062711015-0.1093738165540.2316705622460.02219407084070.1664204278280.1496605442760.08625817821180.07408601801190.30204116608-0.03055844437960.322943051479-0.00930542790158-0.05078975776960.4951399780290.03340930678530.28200492796670.0376827965-2.2753415322117.8792597797
62.066691905030.19520262702-0.5828180787631.232608768710.1041080162480.6735142080860.0840004732613-0.07227837410630.05799137809270.003517070249730.0108824497577-0.072746634406-0.0387900669670.193453198194-0.06196318114840.3173545989690.0146976826722-0.005302769788950.3703949400690.04454805062830.25802841901160.5597987819-7.5812893046719.5706627082
75.78886577191-0.909168463839-2.041086214352.22556920134-0.5066989084293.977409118640.108190832203-0.191280613072-0.3355532983290.0468941645129-0.0307527678356-0.1227794808440.291063909020.596668669315-0.07409662401060.3592350877230.0084794711578-0.05288339794660.4686655773410.007414962671350.29941251259164.638477918-9.6187533776827.1047597135
85.74709290507-1.72796535448-1.532750742822.163055116131.248187947852.42856562677-0.1768244270620.168500538987-0.1791928834890.09932351457910.212927737384-0.1962693339510.343470360980.458540330542-0.02264094331110.3333287338170.0451502899829-0.004864621858110.471463604055-0.0009441816951630.24658991907669.0012020003-11.357530814416.4979562167
93.58077076595-0.312703701075-2.463472534790.8371667020310.4774850930471.616597837390.00903764079058-0.1075501393510.0941480085792-0.1701241207660.0965382777376-0.2807296637260.0737800740290.227231077967-0.1097585595970.370143746160.0361547957887-0.00608992803990.470188082680.01933800057590.32750322759178.2587032357-7.565299983457.43502950906
104.484220757960.269523665312-0.06526159277532.062319051860.03639213137544.835023610440.108794692171-0.2047642770790.642907691225-0.152060369171-0.0082526289201-0.413493034429-0.2270369446460.588591847787-0.08227177212130.4372762238310.038604681630.1103752620030.394386827539-0.03966241072050.53654868069788.3746013046-6.155228955360.0079592219073
115.70779264907-0.03794688469530.9048552595317.954765015570.7311656266038.213616764680.0902081828812-0.7608073707430.6914415800230.101726202584-0.646982344421-0.798000918139-0.5077002267911.048694384740.5846554299230.462445290894-0.1227369511550.07515423622490.74437365963-0.04309448281230.93698423482199.3752439024-4.257135233992.94345836801
123.151887121970.0919753944474-2.060486169961.79223863936-0.4309486593132.186773356410.02624145598480.2553646302290.0543426237556-0.339717366423-0.0004448511016820.2309894154880.244930210251-0.460067853326-0.0274693440770.41688392923-0.0319462949751-0.06793176213260.4864306541250.05317968773370.28654084705449.3864609881-7.396286452040.0953315925897
131.66680184464-0.0142689480276-0.3717572195241.3128754085-0.2018543946911.175647723360.1303617464360.07385732764530.0316197691631-0.204199927244-0.0202013689996-0.2282667259130.1409839949620.199626379136-0.1121144702650.4585115621310.0265374896715-0.006627795235450.268498469682-0.03648804022690.26910194521469.5831281297-10.6773729541-3.27568704536
142.358213123130.05242693670940.8464659040542.01774569541-0.01174380623672.979723633010.1604874572210.144862922851-0.325329075705-0.3872308772860.0561687494448-0.003518121440190.5240968784060.226945435789-0.1657917259130.5531790250950.06641124591350.03076095237340.295200089116-0.03930638317910.26560211488577.1064230196-13.7295635035-10.9810175831
153.33488148676-1.784536417260.1145096051266.394306084930.03749896397281.90673889491-0.01740992723730.188478722432-0.3727932265780.631966755906-0.18346360634-0.1069829596330.4448375300730.01528811231970.2088543121260.294305731096-0.0440902565669-0.02069298722270.233748315063-0.00121634349650.37801956678511.9899498032-11.506255124234.5651766786
163.16973690725-0.6743145813970.8324340423043.61785992303-0.4432331846353.86874196419-0.222411538567-0.1086795262930.5935450641770.42036825557-0.2368720392180.720201058384-0.808964098768-0.8696445142870.4333922922910.6159072728770.09201783446050.04212260109580.371146780744-0.09507925006950.6871367537482.8010608579411.420513232739.6372151197
172.42513111812-1.41827587724-0.5758509792464.315531342891.688218582472.10208150165-0.0448253214090.28047063740.27107124951-0.0249225077398-0.111109172511-0.115394586263-0.40924495033-0.06825437928470.1483572206410.401416294713-0.0535283734778-0.04580513362150.2916166342570.01155619713380.359983463649.80618165348-0.15953420328633.3311360588
186.1638709601-3.78269617373-0.9370150021364.865871053510.9727895523532.54912997887-0.006788801763230.669300000307-0.167241048823-0.563348031863-0.2379864244620.313832410327-0.0985891997169-0.3327162380880.2160790805960.411692314578-0.103025090449-0.05668191288290.4098399216530.01728572343990.3553466036228.36415496702-8.1414837528925.7780118841
192.00541394290.4149887988710.08602419166082.22838891169-0.003829257463023.02254037035-0.1098466571680.813387047880.693806147139-0.83002309940.03607877622440.263136081526-0.08172950272710.1482347669940.1182294007880.6008782681060.0235928817184-0.1157765203350.482801588360.046167634590.4773860390223.008377196491.5675296899124.0400654349
204.63944676093-2.017568709190.8813420893145.80781431629-1.89677529414.44943025471-0.1160780305370.3509256539030.0947601864352-0.4658793891960.265386986359-0.04454954908250.3178322029090.0580743310817-0.1196759114880.402878234213-0.07543735308460.02490802999440.322504877899-0.04585610543960.35613627520622.4762488182-8.5466039156930.0766401504
216.3460057511-3.69846408042-0.5708669970255.050379803270.9078963909282.524269420650.02845808769240.3063966709150.658729485062-0.407244356189-0.0375988460185-0.0459353920892-0.456512720052-0.2238095938410.02928427868940.43546873721-0.0386254073654-0.05518768516550.3204374992860.004153914029610.38838160382210.38425101541.2517172939929.7400668387
220.675437014344-0.451664656199-0.2058377464030.307550861810.1456662069520.06911469847390.3214503454810.3064715030230.611295126119-0.0974433333116-0.1006621104520.808948153811-0.0857059074525-0.34442921704-0.1887004851760.5092406592850.127143959638-0.1198023379850.543757077839-0.1082611424781.09516159342-6.629637319425.8864212825935.2164521465
233.19127907445-3.0344214689-0.7850764429836.22346828963-0.3800990762261.731408124630.1831124231830.387667685821-0.207438424695-1.13698313602-0.5775075450090.900991382657-0.01466569475-0.4185076014210.3648299341930.352793656766-0.00947215621488-0.1143115464540.410098563764-0.1118467065130.4681228176614.23962316881-11.541005228728.3040779607
246.91259226281-1.14206804821-0.4017139931619.504192421193.098864488698.618161779020.452253547239-0.8399361549740.6162563538260.676125040068-0.2670455489530.666622613188-0.6431416894-0.656766067558-0.2550286314950.416730306218-0.05166284793090.08561547866770.5191575530570.008976263737550.5447159339790.0430079216315-2.4538892374938.5004068309
252.016650102610.364637481155-0.514580368542.43411469696-0.4259042519251.425615165060.01833736010320.0009834595730120.26352924491-0.0272159429666-0.008055524935690.074167509684-0.1173310514160.00537642453576-0.0001923280622470.1847134328660.0365344021347-0.03424124752080.284982698171-0.01282453780980.288037468568-9.84136739889-25.130245496748.7471105267
261.13903028118-1.089672558930.01600873305652.23323751333-0.7960883832711.196672938590.1581922136730.18425377299-0.317410489616-0.00253089440745-0.0817622153007-0.418970844660.0585818132316-0.0131289150662-0.07685194384160.2212325852470.03737670298890.02202967085870.256492534124-0.007729026690590.158907331848-5.4655945542-32.817662294442.6993470373
272.370882548410.398763647178-0.8690462838232.220254916550.1508996267342.37521899683-0.03496644797440.4293400995340.462837465271-0.263906238560.02975617967780.0216533114872-0.5077936614470.205598460187-0.003097914828170.386436370735-0.0438905249336-0.1196166909930.5105030082010.06267126461110.444635604279-30.5225515918-24.257080636320.871723949
282.13972656488-1.178908487410.01890370222041.65411661661-0.2098470186591.75817053075-0.0033336473962-0.100076073567-0.139929890383-0.03810112938880.08175012068150.07170913685730.158990075648-0.0446022919595-0.07124682135010.2012546957850.005449215508530.01315181266650.23408797243-0.007934966837120.27821120411614.0212429187-46.891325295555.1703421729
293.14694974644-1.460715948231.276852249711.73444675034-0.5245155419362.32638057618-0.062754550016-0.0380279571860.140121937526-0.044089413289-0.00520459280829-0.129277533303-0.02613474667480.06910795336330.0632159581690.2131879034640.001973371884170.007244277544310.20387813516-0.01282479762530.26400616655616.0915207989-45.733411149753.9293521426
304.71972118282-1.009515045581.705838383513.078572090871.105061056891.365049857610.09873237943280.5875819876050.193597564421-0.0328822572538-0.281680906346-0.3334149655440.3590384719610.4003554818270.1854141752750.276137105970.05084739529990.02009279944360.289113897868-0.05305797723140.40222826247343.4064463285-58.298086133268.7365193742
313.57441846565-0.794348377314-0.7080662827643.051401039541.239155008954.30760053224-0.02387383237490.0775513774064-0.2763098969490.458952131835-0.00236005450032-0.03452891994740.4304249961070.003756550076950.03296644731630.3471907828950.0232189423569-0.009851787310390.218347406586-0.02756052731550.33936014587837.1673106428-60.442507514876.9614964182
321.94682252431-0.0652695724272-0.354492312772.48132115504-1.346510009582.131697239470.00753260402447-0.3084167618110.1715723474910.349223279664-0.122653405827-0.14817972224-0.4162930469640.05470867542840.06943842978980.2734540441980.0238570392093-0.01492920739610.390013055547-0.03524751262340.2855930139537.00194478778-35.435262995876.0106968802
332.45951602533-0.137733913143-0.598961304372.4203297906-1.016716855512.33509743297-0.0555955832107-0.151171108143-0.00790490548570.04134213058230.006437666950830.163987171238-0.108617111151-0.2415218776220.05279174274470.1948917291520.0320207874032-0.01637838664020.272346949984-0.04773660768010.2272056638082.09816281095-37.04058633570.4364031389
342.9217459486-1.127467623291.757981631121.47413119815-0.7202347231192.458946975020.0366254615591-0.00681062130058-0.31334508279-0.1874007160660.03259312587950.1338937654730.419050786088-0.579344459373-0.02015660484790.286410423151-0.008659304450160.03424252867740.385413384888-0.007698229814670.29274453211.7253648205-49.567566335888.141264665
353.92879716603-0.226566339092-1.260024088512.248696403130.5714759163653.214261114520.0643849322610.271069640407-0.09428903472590.113012708713-0.05617886513430.110532704984-0.0828949067563-0.198484619405-0.00458002704620.2720726940450.0372926954961-0.00746324736720.207909923375-0.004553594302950.21783360867933.3945012453-50.118164013581.1035741703
364.682669741590.752208251308-2.267987915350.6820840884790.07072619023151.641964173330.337156443075-0.02177777967340.2017928483320.0577878368806-0.105040789702-0.0662692458453-0.259713899462-0.0673360800764-0.1793776441780.3224160745440.0370871836431-0.03532455561170.293086202218-0.03437002316290.286354015729.0214105983-43.760514249191.407924279
372.24733961265-1.77610185083-2.660974012555.900351532850.6667768102195.299972498960.000466458468639-0.3613536950131.27956920539-0.4027585229160.276710100682-0.473091572425-0.5397724165350.53174926893-0.2914431821540.612778714406-0.020635215308-0.04337045236690.5481844843660.05081114732170.941568374948-15.878404556-7.2373878945541.1874176923
383.05884733732-0.527520777641-0.5695061978581.81355578979-0.1137202948241.76169123059-0.2571153901690.3304330777450.472979232129-0.2766572425830.1298728238860.896377204483-0.00593418820076-0.5859462582470.1497385716690.4021377613190.059132183997-0.1585768800630.60272090592-0.04315794994610.735005928983-36.1658508344-19.707361791637.9565439358
392.89452064446-0.1068895361351.074875501280.16088891437-0.3398723724990.947437477053-0.233308243923-0.8473489818190.8549340934530.1131399174180.005212423160260.508273691137-0.520297446375-0.2941772358090.1943565535050.473530620420.170597112485-0.1022977971840.618484790561-0.2180204453260.861085931943-28.7339370767-11.140003650447.3752842306
406.1488686429-1.69489628752-0.001896430301811.11457570350.7362028155241.245549147090.00373086910583-0.4532140356-0.1131537966480.277724104519-0.1398656938810.879015167919-0.140429724695-0.3039672227320.116852261140.524993237340.2193503237510.08023991801230.861310302112-0.03855496963090.984066991653-38.9503054078-14.80736713549.5499750316
417.5707054111-0.764469269918-4.68030179073.568170161280.3411245888175.22601226709-0.209795291339-0.564479877083-0.5765850203230.1780230520840.06090528142710.191441217993-0.5020342519190.3214884210720.1429162187140.4328808376110.0297775271434-0.1152801135240.514874263585-0.006939827111230.437695859416-21.7068149913-21.878749417747.5118456396
422.12408774972.329156866140.8970911424725.31993553594-1.39063406667.621611914540.1013282342380.5010990342730.096563211479-0.4603156050450.326580912890.5908943903810.0230049514294-0.617587042304-0.4206984497720.3137322981550.029616102281-0.09768434677240.3423645112670.008955809834010.477462727073-13.4436438041-18.659678898539.9455093955
432.03577794044-1.02928645175-0.5045973808381.433648353960.09620622740882.33166191182-0.598744711777-1.043544201390.2821556937450.2072856892450.18927394360.5077190433170.131828517552-0.5347737917620.4177271260680.3831973542090.0695306183736-0.01411454862080.612308429196-0.07005710713660.658278944914-33.2936095704-20.098521079744.3558603262
440.000318924271938-0.00103857985287-0.001694540240690.0007827850580950.002098389603780.000161216057393-0.401005952708-0.3197634157450.416201646509-0.240531512487-0.3059824618220.366863332624-0.538865860673-0.3695333524920.6517503850270.6059538743870.133329059272-0.3029041289041.19332400854-0.02165252690281.21515234958-49.5162828379-13.955801552638.4635929987
455.149646502160.1979482636980.5375816297750.9446369479630.4129200678421.950911631090.240625927883-0.2815802438310.5315211245250.06394327143110.3242915704880.0572949992238-0.2148397971050.0213956213553-0.44068894650.3853417986210.157020036314-0.02691532749710.621825953294-0.20463502171.35545685297-35.2577503857-9.3658490012743.8998903802
463.39700260038-2.967040185841.293821595212.5911633783-1.134038447650.496543543920.0549091368843-0.03080803997810.2595121024710.166989423959-0.0383080093230.836124776165-0.62810054629-0.483148857591-0.04034541875080.5457887503950.130251843679-0.1113058584660.567486541905-0.164559171221.26640031845-24.4478114293-2.9162474203144.6743189521
472.302530597342.53999456876-0.2243112109236.338053835570.8442904000551.41815840222-0.1450941203920.1700161054170.131825888405-0.608008489748-0.07627432187280.0620601717064-0.10112389234-0.1391615087450.1611022956940.5527296606550.206910846409-0.2599770461190.500310596927-0.04320282788881.15171143412-36.993102257-9.5237149471736.7765618238
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 'C' and (resid 1 through 83 )CA1 - 831 - 83
22chain 'C' and (resid 84 through 171 )CA84 - 17184 - 171
33chain 'C' and (resid 172 through 237 )CA172 - 237172 - 237
44chain 'C' and (resid 238 through 270 )CA238 - 270238 - 266
55chain 'D' and (resid 1 through 17 )DC1 - 171 - 17
66chain 'D' and (resid 18 through 52 )DC18 - 5218 - 52
77chain 'D' and (resid 53 through 75 )DC53 - 7553 - 75
88chain 'D' and (resid 76 through 91 )DC76 - 9176 - 91
99chain 'D' and (resid 92 through 135 )DC92 - 13592 - 129
1010chain 'D' and (resid 136 through 188 )DC136 - 188130 - 181
1111chain 'D' and (resid 189 through 199 )DC189 - 199182 - 192
1212chain 'E' and (resid 3 through 94 )ED3 - 941 - 92
1313chain 'E' and (resid 95 through 140 )ED95 - 14093 - 138
1414chain 'E' and (resid 141 through 244 )ED141 - 244139 - 242
1515chain 'F' and (resid 0 through 11 )FE0 - 111 - 12
1616chain 'F' and (resid 12 through 19 )FE12 - 1913 - 20
1717chain 'F' and (resid 20 through 30 )FE20 - 3021 - 31
1818chain 'F' and (resid 31 through 41 )FE31 - 4132 - 42
1919chain 'F' and (resid 42 through 51 )FE42 - 5143 - 52
2020chain 'F' and (resid 52 through 61 )FE52 - 6153 - 62
2121chain 'F' and (resid 62 through 71 )FE62 - 7163 - 72
2222chain 'F' and (resid 72 through 77 )FE72 - 7773 - 78
2323chain 'F' and (resid 78 through 90 )FE78 - 9079 - 91
2424chain 'F' and (resid 91 through 99 )FE91 - 9992 - 100
2525chain 'A' and (resid 0 through 133 )AF0 - 1331 - 134
2626chain 'A' and (resid 134 through 182 )AF134 - 182135 - 183
2727chain 'A' and (resid 183 through 270 )AF183 - 270184 - 264
2828chain 'B' and (resid 1 through 52 )BH1 - 521 - 52
2929chain 'B' and (resid 53 through 108 )BH53 - 10853 - 108
3030chain 'B' and (resid 109 through 120 )BH109 - 120109 - 120
3131chain 'B' and (resid 121 through 200 )BH121 - 200121 - 200
3232chain 'G' and (resid 2 through 37 )GI2 - 372 - 37
3333chain 'G' and (resid 38 through 109 )GI38 - 10938 - 109
3434chain 'G' and (resid 110 through 124 )GI110 - 124110 - 124
3535chain 'G' and (resid 125 through 202 )GI125 - 202125 - 202
3636chain 'G' and (resid 203 through 244 )GI203 - 244203 - 244
3737chain 'H' and (resid 0 through 5 )HJ0 - 51 - 6
3838chain 'H' and (resid 6 through 30 )HJ6 - 307 - 31
3939chain 'H' and (resid 31 through 41 )HJ31 - 4132 - 42
4040chain 'H' and (resid 42 through 51 )HJ42 - 5143 - 52
4141chain 'H' and (resid 52 through 56 )HJ52 - 5653 - 57
4242chain 'H' and (resid 57 through 61 )HJ57 - 6158 - 62
4343chain 'H' and (resid 62 through 71 )HJ62 - 7163 - 72
4444chain 'H' and (resid 72 through 77 )HJ72 - 7773 - 78
4545chain 'H' and (resid 78 through 83 )HJ78 - 8379 - 84
4646chain 'H' and (resid 84 through 90 )HJ84 - 9085 - 91
4747chain 'H' and (resid 91 through 96 )HJ91 - 9692 - 97

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る