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- PDB-9btx: Structure of human MAIT A-F7 TCR in complex with human MR1-3,4-di... -

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基本情報

登録情報
データベース: PDB / ID: 9btx
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-3,4-dihydroxybenzaldehyde
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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / endoplasmic reticulum membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
ACETATE ION / Protocatechuic aldehyde / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.05 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8日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
改定 1.22025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)189,38825
ポリマ-188,1008
非ポリマー1,28817
14,970831
1
A: Major histocompatibility complex class I-related gene protein
B: 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)94,81614
ポリマ-94,0504
非ポリマー76610
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-59 kcal/mol
Surface area36210 Å2
手法PISA
2
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,57211
ポリマ-94,0504
非ポリマー5227
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-52 kcal/mol
Surface area35170 Å2
手法PISA
単位格子
Length a, b, c (Å)217.129, 70.405, 143.573
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11A-539-

HOH

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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 , 5種, 848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: 6 / 由来タイプ: 合成 / : C3H8O3
#6: 化合物 ChemComp-H6N / Protocatechuic aldehyde / 3,4-ジヒドロキシベンズアルデヒド


分子量: 138.121 Da / 分子数: 2 / 由来タイプ: 合成 / : C7H6O3 / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 7 / 由来タイプ: 合成 / : C2H3O2
#8: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 2 / 由来タイプ: 合成 / : Na
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 831 / 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: 2.82 Å3/Da / 溶媒含有率: 56.43 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG3350, 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: 0.9536 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年3月2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: 0.9536 Å / 相対比: 1
反射解像度: 2.05→36.19 Å / Num. obs: 427544 / % possible obs: 97.48 % / 冗長度: 3.3 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05743 / Net I/σ(I): 11.71
反射 シェル解像度: 2.05→2.123 Å / Num. unique obs: 40598 / CC1/2: 0.772 / CC star: 0.933

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
XDSデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.05→36.19 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.93 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2177 3275 1.34 %
Rwork0.1854 --
obs0.1858 244108 94.57 %
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
精密化ステップサイクル: LAST / 解像度: 2.05→36.19 Å
タンパク質核酸リガンド溶媒全体
原子数12579 0 84 833 13496
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00313325
X-RAY DIFFRACTIONf_angle_d0.58618202
X-RAY DIFFRACTIONf_dihedral_angle_d20.154798
X-RAY DIFFRACTIONf_chiral_restr0.0431956
X-RAY DIFFRACTIONf_plane_restr0.0042376
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.381380.361510234X-RAY DIFFRACTION92
2.08-2.110.38621350.33649895X-RAY DIFFRACTION90
2.11-2.150.34151460.320210386X-RAY DIFFRACTION94
2.15-2.180.35441400.306310453X-RAY DIFFRACTION95
2.18-2.220.34681400.291910305X-RAY DIFFRACTION93
2.22-2.270.31961470.281210514X-RAY DIFFRACTION95
2.27-2.310.26671460.27310577X-RAY DIFFRACTION96
2.31-2.360.33561430.270610650X-RAY DIFFRACTION96
2.36-2.420.28351440.250310556X-RAY DIFFRACTION96
2.42-2.480.3261420.245710611X-RAY DIFFRACTION96
2.48-2.550.33381490.237210630X-RAY DIFFRACTION96
2.55-2.620.27561450.231910651X-RAY DIFFRACTION96
2.62-2.710.26151390.220110607X-RAY DIFFRACTION96
2.71-2.80.2771390.224910543X-RAY DIFFRACTION95
2.8-2.910.22371450.20910397X-RAY DIFFRACTION94
2.91-3.050.23691360.200610039X-RAY DIFFRACTION91
3.05-3.210.25321380.190810428X-RAY DIFFRACTION94
3.21-3.410.21721370.174710515X-RAY DIFFRACTION95
3.41-3.670.21771480.15710745X-RAY DIFFRACTION97
3.67-4.040.16541470.151810691X-RAY DIFFRACTION97
4.04-4.620.15761450.12610625X-RAY DIFFRACTION96
4.63-5.820.15481380.1410267X-RAY DIFFRACTION92
5.82-36.190.16971480.165710514X-RAY DIFFRACTION95
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)
11.27260.1057-0.47340.94960.95941.46110.08840.14910.1451-0.23310.0721-0.09590.07230.2797-00.2911-0.0341-0.01450.3915-0.01210.425349.234777.7205224.352
21.0585-0.0613-0.2041.17630.72290.52190.0672-0.08780.21410.01690.00310.20010.03990.010300.3519-0.0047-0.00970.35050.01610.47736.901280.8445235.1249
30.4419-0.36620.27670.5596-0.40580.5778-0.0971-0.09440.08960.180.1665-0.12930.11010.1349-00.36710.1193-0.07430.6172-0.1570.483762.950374.511247.1907
40.26320.0129-0.24140.3278-0.33890.4326-0.0684-0.45950.16570.08840.07550.1051-0.22710.05080.00070.48750.145-0.09930.7779-0.25690.555568.752779.9348260.2247
50.0086-0.0128-0.02810.05010.05390.04920.20670.01750.37780.36450.58910.2089-0.2654-0.079800.6273-0.0576-0.01670.6651-0.04441.100752.29297.1882236.0896
60.01990.0374-0.03440.039-0.04360.0333-0.2979-0.1362-0.21380.61880.093-0.1841-0.04850.33450.00010.4488-0.0076-0.13020.7487-0.16910.833968.715788.5203240.6182
70.00670.02650.04340.02880.0490.5421-0.5157-0.269-0.10210.4645-0.0547-0.26610.28880.5237-0.01260.41250.0134-0.21080.9694-0.07730.920681.853380.1838241.2841
80.01520.0787-0.00810.1998-0.11040.06850.12210.09770.3098-0.29030.162-0.133-0.42650.58650.06470.3315-0.0516-0.07510.7916-0.13640.718269.184185.5907236.1416
90.0433-0.0286-0.14920.02660.10290.56710.30380.18440.1231-0.0262-0.0989-0.151-0.5516-0.16820.05360.3906-0.16920.01110.54580.03660.808264.161393.213229.7136
100.0498-0.0011-0.03730.0374-0.06350.07440.10630.39810.2758-0.6033-0.1867-0.23870.0852-0.109300.5654-0.09970.01351.0705-0.06660.914675.269389.5854227.1085
110.04280.0278-0.0361-0.0089-0.017-0.01720.35440.18130.08490.0063-0.1577-0.1025-0.17240.36380.00010.3987-0.00250.01530.4531-0.04750.528654.003984.1336233.6611
120.07140.1598-0.09080.1585-0.13110.0757-0.21140.2850.3751-0.03820.1636-0.15920.07080.1882-00.3189-0.07650.03980.6821-0.12350.6269.731184.3327232.4827
130.93110.1050.12421.4133-0.17281.13380.2216-0.03860.07420.03910.41010.0665-0.1946-0.07550.26750.4327-0.0714-0.23681.5879-0.24341.241786.191390.4882237.9571
140.04220.0410.08770.05630.06270.14840.20420.02420.0859-0.0298-0.0103-0.81470.09260.57490.17040.4404-0.1691-0.04830.69940.05961.266965.937298.3938232.5127
150.02650.0322-0.00670.0689-0.0037-0.0067-0.4463-0.0703-0.17830.4937-0.03540.27280.26670.1695-0.00260.601-0.2323-0.15660.9577-0.1370.906972.74595.1615239.7624
160.90720.2066-0.0681.8976-0.02161.61750.03080.1667-0.04190.0454-0.17610.0984-0.08130.01300.355-0.02740.00970.4842-0.06020.352-4.172759.5263164.835
170.6192-0.2723-0.19730.25230.04220.9392-0.05360.0875-0.04370.0368-0.02520.1495-0.18110.0262-00.3765-0.04630.02910.2639-0.01830.3838-12.501468.678184.6777
181.13480.5051-0.13640.26260.44961.3688-0.05990.11030.08460.07350.04-0.04430.00560.1743-0.00120.3917-0.1019-0.00640.60750.1560.340829.762762.3028159.1924
190.6221-0.05610.49750.00880.08190.27170.0317-0.6240.1273-0.08850.1923-0.54090.00850.31210.00010.6914-0.03940.05471.01660.03430.776252.936561.4494139.3621
200.06120.0873-0.03380.0565-0.03920.0035-0.44560.04840.41620.11490.4222-1.0236-0.15220.67510.00040.7793-0.10470.03141.12110.03360.968360.599467.9002136.9062
211.3944-0.7541-0.18460.3945-0.27811.0552-0.07320.4610.1394-0.0975-0.15040.0867-0.0779-0.0739-0.0170.4612-0.1612-0.03390.76410.11710.316613.565662.5906139.7617
220.1096-0.0390.09390.155-0.0740.0566-0.0388-0.152-0.12530.229-0.2023-0.04-0.4587-0.02420.00010.4706-0.09590.06560.70830.04180.452114.179755.8756153.0495
230.4646-0.23430.26290.1716-0.22740.40640.57060.05-0.0777-0.13260.57470.4503-0.1278-0.45181.66650.4879-0.3870.41191.10910.5762-0.515428.146966.9688125.3242
242.63881.04021.81580.79010.52742.17890.5315-0.0219-0.7251-0.25560.09190.04280.5338-0.01221.79410.6093-0.0652-0.01830.70230.09220.476546.234156.5233132.6529
250.4809-0.1002-0.27561.3315-0.81161.35290.44280.693-0.97110.07580.35420.33030.3488-0.13520.33270.8431-0.187-0.26520.9125-0.09660.697136.271353.0677124.0457
261.4684-0.208-1.0991.2172-0.48941.32990.74140.4271-0.0204-0.75290.2559-0.3388-0.01210.01130.52630.9224-0.2092-0.19310.8756-0.14310.434437.434855.5338119.7889
270.0219-0.0436-0.00420.01290.0079-0.00550.21080.1959-0.36130.0120.0169-0.00180.2820.4182-00.46520.0382-0.02870.4582-0.1850.6039-20.401249.1721171.2972
280.02060.02860.01520.01740.01730.0016-0.24980.2864-0.13210.06120.441-0.3017-0.54280.1417-0.00020.4212-0.0318-0.04670.3546-0.01970.4363-27.792465.9718176.9648
290.0061-0.010.01710.0089-0.02290.0185-0.181-0.00690.3236-0.549-0.18420.3514-0.55470.2264-0.00010.69980.0976-0.12070.4072-0.05460.7785-32.888579.9225178.6446
300.05820.0045-0.00420.03940.0655-0.0566-0.15660.58620.0134-0.053-0.08310.0693-0.28080.062600.45780.0028-0.03520.3892-0.04820.4886-26.27968.8907172.9261
310.1010.14480.02810.140.00260.1052-0.22880.3964-0.0466-0.12520.09120.0317-0.16190.03300.53560.0155-0.07840.6576-0.12510.5392-27.420560.9823165.549
320.035-0.0140.0440.0360.05230.05-0.14610.39030.1327-1.270.00450.3102-0.09330.1071-00.79270.0148-0.14620.8980.05360.8007-32.876770.6536163.431
330.00330.0125-0.00160.018-0.03120.01530.15280.06570.08730.02430.0718-0.07010.03290.17260.00010.6293-0.0211-0.00480.6783-0.08260.4972-15.615864.6246166.2426
340.33370.33940.01330.23480.01620.2093-0.2665-0.1046-0.0395-0.35410.45070.0829-0.1560.0793-00.4566-0.0349-0.01910.508-0.05170.4313-21.468266.2699170.67
350.00720.00510.01560.03530.01410.0070.0463-0.03130.19640.1629-0.56690.09370.0859-0.22130.00010.7940.2182-0.08530.8654-0.08121.1179-43.075474.3656174.6866
360.0328-0.05340.00920.02360.0291-0.031-0.08550.6083-0.1273-0.8835-0.04550.2052-0.2129-0.1388-0.00020.41-0.0241-0.09230.5261-0.10520.6022-32.016257.3614167.8096
370.04940.0551-0.08930.0947-0.12080.1030.0068-0.25890.16280.3682-0.13120.4389-0.3418-0.23820.00010.51350.02990.01360.622-0.1170.6087-36.194166.6273177.9135
380.0568-0.0916-0.06220.6982-0.19910.21310.04910.2299-0.02510.09650.0731-0.14330.16360.0892-0.00010.3739-0.064-0.00550.31780.00860.409420.126650.6465220.5652
390.5136-0.0931-0.19610.45410.25730.3096-0.06690.00470.1160.0620.27980.0260.08190.07230.00790.3578-0.0576-0.03030.23540.02840.375124.536360.4784222.5001
400.25270.37620.09850.73230.20640.4067-0.0325-0.08820.11330.08070.04610.09290.0346-0.189-00.4089-0.04930.01440.3420.01910.404618.160858.8842225.7662
410.08770.54540.23460.591-0.00340.73590.2225-0.5101-0.25290.1187-0.1409-0.07310.0408-0.1132-0.00180.3684-0.04820.02060.3394-0.02030.369212.483952.6468214.6335
421.70590.2741-0.18921.0352-0.66591.4075-0.0228-0.0875-0.1455-0.1705-0.0571-0.00090.15320.0221-00.3992-0.03740.0150.22210.02760.36370.52244.6725198.9261
430.0144-0.05620.01660.1146-0.07240.04490.2238-0.0149-0.4325-0.4234-0.1685-0.02780.54070.0039-0.00010.465-0.05820.05950.40.09050.4911-5.080535.8678203.7067
441.03230.26730.47160.45660.48890.6379-0.13080.34660.2754-0.0460.01380.095-0.07160.111600.3794-0.1074-0.01850.42010.07060.36630.254166.5556203.0186
450.36240.0929-0.04560.3560.38450.2596-0.26970.40690.0807-0.11670.4203-0.2090.00870.51320.02240.4734-0.138-0.0490.59750.08170.449638.955671.087205.3297
460.73070.0568-0.06060.58050.12690.0418-0.18050.1190.0750.02460.2501-0.10350.00610.465400.4037-0.0666-0.02740.47680.03120.410131.485666.8074206.9117
470.0116-0.07490.00880.09460.11260.050.0472-0.0474-0.17640.19080.00390.09220.38440.7868-0.00010.4182-0.00310.00080.55680.01620.413625.151153.5527188.3488
480.1053-0.1030.12430.0412-0.11390.10850.2768-0.20130.0856-0.2623-0.07710.222-0.1492-0.02290.00020.4157-0.04290.00410.3160.02430.396-7.771950.1763195.21
490.1503-0.18070.13810.3642-0.34740.46630.2251-0.44580.04880.0412-0.20790.0579-0.18590.1898-00.3841-0.08250.020.32520.01150.34676.970356.0216193.9649
500.55220.4516-0.37130.3837-0.14660.39350.1723-0.3592-0.0262-0.1142-0.1518-0.2522-0.08890.32950.00010.4676-0.0123-0.00020.41280.01540.381910.410952.7468196.8748
510.09380.11630.00020.15750.1710.0980.2387-0.1345-0.1934-0.0533-0.21140.0653-0.14960.18810.00010.4022-0.06580.04320.23510.05180.3497-2.277455.0891197.6841
520.0691-0.0364-0.15520.12230.0560.33630.1409-0.13260.334-0.31390.10090.1363-0.1350.12170.03170.4857-0.05660.03170.25060.04040.4291-2.896862.1869190.2334
530.1592-0.14370.01470.1443-0.13930.10720.1164-0.3497-0.02270.1269-0.0131-0.19170.14970.9685-0.00010.459-0.07-0.03590.54460.08190.431223.474758.457180.1666
540.0221-0.0071-0.06460.17290.17940.1541-0.11630.24460.0598-0.2777-0.07640.0581-0.2329-0.37550.00010.4751-0.0798-0.04630.48360.00530.4207-2.675159.26186.7567
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 237 )
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 19 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 30 )
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 61 )
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 77 )
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 96 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 133 )
17X-RAY DIFFRACTION17chain 'C' and (resid 134 through 270 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 116 )
19X-RAY DIFFRACTION19chain 'D' and (resid 117 through 174 )
20X-RAY DIFFRACTION20chain 'D' and (resid 175 through 198 )
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 94 )
22X-RAY DIFFRACTION22chain 'E' and (resid 95 through 109 )
23X-RAY DIFFRACTION23chain 'E' and (resid 110 through 124 )
24X-RAY DIFFRACTION24chain 'E' and (resid 125 through 203 )
25X-RAY DIFFRACTION25chain 'E' and (resid 204 through 225 )
26X-RAY DIFFRACTION26chain 'E' and (resid 226 through 242 )
27X-RAY DIFFRACTION27chain 'F' and (resid 0 through 5 )
28X-RAY DIFFRACTION28chain 'F' and (resid 6 through 11 )
29X-RAY DIFFRACTION29chain 'F' and (resid 12 through 19 )
30X-RAY DIFFRACTION30chain 'F' and (resid 20 through 30 )
31X-RAY DIFFRACTION31chain 'F' and (resid 31 through 41 )
32X-RAY DIFFRACTION32chain 'F' and (resid 42 through 51 )
33X-RAY DIFFRACTION33chain 'F' and (resid 52 through 56 )
34X-RAY DIFFRACTION34chain 'F' and (resid 57 through 71 )
35X-RAY DIFFRACTION35chain 'F' and (resid 72 through 77 )
36X-RAY DIFFRACTION36chain 'F' and (resid 78 through 90 )
37X-RAY DIFFRACTION37chain 'F' and (resid 91 through 99 )
38X-RAY DIFFRACTION38chain 'G' and (resid 1 through 17 )
39X-RAY DIFFRACTION39chain 'G' and (resid 18 through 52 )
40X-RAY DIFFRACTION40chain 'G' and (resid 53 through 91 )
41X-RAY DIFFRACTION41chain 'G' and (resid 92 through 120 )
42X-RAY DIFFRACTION42chain 'G' and (resid 121 through 185 )
43X-RAY DIFFRACTION43chain 'G' and (resid 186 through 200 )
44X-RAY DIFFRACTION44chain 'H' and (resid 1 through 49 )
45X-RAY DIFFRACTION45chain 'H' and (resid 50 through 73 )
46X-RAY DIFFRACTION46chain 'H' and (resid 74 through 109 )
47X-RAY DIFFRACTION47chain 'H' and (resid 110 through 124 )
48X-RAY DIFFRACTION48chain 'H' and (resid 125 through 140 )
49X-RAY DIFFRACTION49chain 'H' and (resid 141 through 162 )
50X-RAY DIFFRACTION50chain 'H' and (resid 163 through 188 )
51X-RAY DIFFRACTION51chain 'H' and (resid 189 through 202 )
52X-RAY DIFFRACTION52chain 'H' and (resid 203 through 215 )
53X-RAY DIFFRACTION53chain 'H' and (resid 216 through 233 )
54X-RAY DIFFRACTION54chain 'H' and (resid 234 through 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

他の情報も見る