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

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基本情報

登録情報
データベース: PDB / ID: 9btz
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-nicotinaldehyde
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 / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
ACETATE ION / : / 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: 3 Å
データ登録者Awad, W. / Rossjohn, J.
資金援助 オーストラリア, 2件
組織認可番号国
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. / 年: 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)188,97519
ポリマ－188,1008
非ポリマー87511
水3,351186
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)94,3909
ポリマ－94,0504
非ポリマー3405
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-57 kcal/mol
Surface area36190 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)94,58510
ポリマ－94,0504
非ポリマー5356
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-43 kcal/mol
Surface area35710 Å2
手法PISA
単位格子
Length a, b, c (Å)214.567, 69.621, 143.344
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number5
Space group name H-MC121

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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, 197分子

#5: 化合物 ChemComp-XIE / pyridine-3-carbaldehyde / NICOTINALDEHYDE


分子量: 107.110 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H5NO / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H3O2
#7: 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 / 式: C3H8O3
#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: 1 / 由来タイプ: 合成 / 式: Na
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 186 / 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: 2.76 Å3/Da / 溶媒含有率: 55.43 %
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: 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: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年7月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9537 Å / 相対比: 1
反射解像度: 3→49.84 Å / Num. obs: 169305 / % possible obs: 97.83 % / 冗長度: 4.1 % / CC1/2: 0.99 / Net I/σ(I): 9.06
反射 シェル解像度: 3→3.107 Å / Num. unique obs: 15947 / CC1/2: 0.851

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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: 3→49.84 Å / SU ML: 0.38 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.09 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2548 2077 5.11 %
Rwork0.1925 --
obs0.1958 40674 97.85 %
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: 3→49.84 Å
タンパク質核酸リガンド溶媒全体
原子数12516 0 57 187 12760
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00812952
X-RAY DIFFRACTIONf_angle_d0.99517633
X-RAY DIFFRACTIONf_dihedral_angle_d20.9774551
X-RAY DIFFRACTIONf_chiral_restr0.0511890
X-RAY DIFFRACTIONf_plane_restr0.0082308
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.28241140.22332521X-RAY DIFFRACTION96
3.07-3.150.34961110.23092560X-RAY DIFFRACTION97
3.15-3.230.3081160.24582554X-RAY DIFFRACTION98
3.23-3.330.3491400.23962609X-RAY DIFFRACTION98
3.33-3.430.29471490.22712513X-RAY DIFFRACTION98
3.43-3.560.28021510.19852572X-RAY DIFFRACTION98
3.56-3.70.29011290.19112586X-RAY DIFFRACTION98
3.7-3.870.29231310.19142579X-RAY DIFFRACTION98
3.87-4.070.23051440.1992557X-RAY DIFFRACTION98
4.07-4.330.24661330.16882590X-RAY DIFFRACTION98
4.33-4.660.21931520.15082502X-RAY DIFFRACTION96
4.66-5.130.2261750.15552535X-RAY DIFFRACTION98
5.13-5.870.21461430.17622598X-RAY DIFFRACTION99
5.87-7.390.25811440.20912631X-RAY DIFFRACTION99
7.39-49.840.22421450.19562690X-RAY DIFFRACTION97
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)
10.57560.14780.00170.0026-0.01450.0141-0.18730.50940.04730.04810.0457-0.2241-0.01410.0889-0.04620.3191-0.00740.02060.23160.01140.360853.008578.843228.8553
20.42660.0156-0.15260.23840.18790.17880.00510.0840.0352-0.1348-0.07640.1291-0.00770.0297-0.00020.28890.00190.03320.25540.05530.318242.008879.2003229.3887
30.24-0.134-0.05310.01710.03090.1948-0.03180.3141-0.017-0.21530.23440.02170.2808-0.16730.2282-0.01950.384-0.0085-0.031-0.21460.388362.811273.6628248.4629
40.1088-0.04220.0550.0053-0.04670.146-0.02430.1235-0.0352-0.1615-0.1139-0.00270.06990.108-0.18030.20520.36330.12530.0725-0.38260.188568.553979.9651256.551
50.03010.0035-0.00820.0225-0.01080.09620.08130.0132-0.08960.29690.0994-0.2031-0.00260.12460.07870.5020.2124-0.14990.2506-0.27190.767958.973694.3087238.4283
60.0477-0.019-0.00220.05290.0036-0.0045-0.1412-0.053-0.0252-0.23690.2324-0.1237-0.00990.06120.01670.2525-0.14-0.02170.52710.02050.54474.933883.3938239.0399
70.01830.0090.01750.01290.01770.04-0.03620.0260.1042-0.2725-0.0283-0.0719-0.18140.1941-0.01840.373-0.1677-0.03650.65060.16650.830365.312992.918229.929
80.00820.0002-0.00670.01210.00730.0120.14170.10430.1096-0.0657-0.0632-0.1952-0.1226-0.19920.00010.43160.08160.06260.48-0.06920.67770.987687.1588228.3386
90.02880.00570.00030.2692-0.30220.32770.0949-0.0407-0.30150.07410.182-0.2511-0.04830.07530.09030.3567-0.06660.02650.3947-0.13030.422165.048184.4977234.2777
100.0004-0.00310.00090.0067-0.0070.0034-0.08090.0271-0.009-0.0124-0.0372-0.0721-0.0473-0.02060.00010.63280.25610.08840.6510.0640.865887.111190.8828239.4344
110.0257-0.01240.0124-0.000800.00080.1307-0.00470.0281-0.02070.071-0.2218-0.09460.0601-00.3952-0.0613-0.01390.299-0.03040.725172.875394.783233.3951
120.04130.0598-0.01180.0852-0.0010.02860.042-0.02690.04410.09240.02380.14650.03230.0452-0.03110.2104-0.2948-0.14530.56750.09750.72369.161197.3594237.1597
130.0832-0.0306-0.05340.0982-0.0650.0665-0.14120.06150.2578-0.199-0.13130.3158-0.145-0.04220.00050.4124-0.05760.04260.2937-0.00780.4097-8.339361.4218165.4202
140.40940.1249-0.19380.11350.12940.40480.01710.0166-0.0012-0.0221-0.0300.03020.030100.3368-0.02340.04760.3059-0.01230.285-0.315458.0217165.4573
150.1489-0.11690.26960.17820.04120.3515-0.1755-0.00350.1108-0.0408-0.0738-0.0394-0.3086-0.1564-0.24950.3341-0.12650.09560.2544-0.03520.2319-14.244273.9587184.8311
160.126-0.1198-0.08980.21690.06670.0425-0.2687-0.3420.1077-0.13870.26910.10950.26030.1728-0.00360.34450.0215-0.00620.3811-0.01190.4458-20.164371.3955193.7656
170.03720.04530.04370.1163-0.00630.1040.0820.06380.0017-0.18490.2765-0.0427-0.02210.10720.49150.0422-0.16530.52750.38090.33790.258735.476967.0431157.267
180.02630.0606-0.0410.0479-0.03540.0061-0.23820.15540.2235-0.02230.01940.0334-0.04740.27720.00010.37470.05250.00520.3970.0350.442325.161465.0389160.3978
190.0353-0.03040.02310.0451-0.03650.016-0.18430.0985-0.14050.0676-0.239-0.148-0.1783-0.21540.00110.3651-0.03480.0160.589-0.0390.398725.445157.397156.804
200.01920.0082-0.03150.003-0.02780.01130.04860.0290.1573-0.14930.0396-0.01140.0594-0.082700.37840.02580.0880.60250.01360.374729.147660.6335166.8783
210.1351-0.0408-0.00910.03570.07780.0273-0.1834-0.014-0.2697-0.0412-0.0012-0.1279-0.07930.0507-0.04180.2453-0.10980.08520.5540.04660.304634.331657.9943155.9183
220.1334-0.17850.03730.2653-0.1250.14920.0967-0.03310.1804-0.2527-0.0904-0.41480.230.06860.05410.43-0.1689-0.15680.28850.12790.490717.873167.5265155.9481
230.14250.02040.04320.03290.0190.0422-0.0187-0.40910.23850.10010.0477-0.32270.01550.08320.03820.23810.0070.05610.5451-0.02690.460755.288859.0598142.7845
24-0.0073-0.0120.01550.02060.02970.01180.1177-0.18470.0345-0.130.0774-0.0547-0.21160.085300.7741-0.07850.00920.4007-0.08590.649153.500968.123141.3059
250.01850.02370.04290.2011-0.07520.05310.3177-0.2047-0.15770.27320.1174-0.02530.0904-0.03670.27780.3755-0.02460.08980.50340.39340.515450.163157.2245141.3092
260.02480.0750.04010.42120.13630.10710.33520.1085-0.03330.19470.1598-0.14090.1727-0.06270.05430.3154-0.13070.10780.4933-0.03510.532755.130162.7743135.5671
270.01510.02260.01210.01550.01310.00060.14340.1083-0.0211-0.05450.2002-0.20070.08320.22380.00010.45970.0548-0.02280.461-0.13350.531662.547667.3562141.1342
280.10510.0385-0.0801-0.0239-0.07490.1312-0.05790.34790.1147-0.0138-0.07390.1528-0.0787-0.1973-0.00180.3464-0.06730.00220.51290.00270.271913.936161.294140.1823
29-0.02250.0096-0.01030.0592-0.0508-0.00180.08250.1347-0.01620.0827-0.0081-0.01310.0394-0.1421-00.314-0.0270.02980.36580.03910.272816.288161.2454142.8107
300.13850.0052-0.03660.0716-0.03930.14130.2870.0177-0.6548-0.41920.21130.18220.08030.06780.03010.29830.05310.07290.4199-0.06130.383643.107758.0819129.5122
310.3612-0.00560.14960.663-0.30750.19520.20960.2279-0.3446-0.14330.25760.15860.19040.33980.35470.30320.1042-0.02740.2595-0.20680.276741.839655.3346127.6385
320.05340.0139-0.00840.0245-0.04910.0685-0.0024-0.01690.22280.0134-0.0613-0.1103-0.37820.0308-0.05730.27430.12470.051-0.349-0.05180.5682-23.869159.3423174.7664
330.0395-0.00140.09010.00250.01210.1913-0.09780.01590.02060.0841-0.0965-0.0763-0.02770.1326-0.07360.48170.2388-0.14280.2218-0.28490.9955-32.272880.4866179.1328
340.0199-0.0269-0.04250.0084-0.00030.0391-0.15840.18970.0089-0.08630.04780.01790.0574-0.11090.00030.3169-0.00480.02350.3022-0.00440.2583-25.429569.3145172.9028
350.00020.0048-0.01180.01870.00030.01490.00850.2322-0.0526-0.1180.1205-0.05420.0624-0.0060.00420.36810.0585-0.13330.44810.03730.4642-26.758461.3702165.1959
360.0152-0.06140.04470.2409-0.1640.1096-0.0583-0.00840.0406-0.1745-0.066-0.1221-0.0287-0.0857-0.00720.4505-0.1638-0.25460.52330.03870.6666-38.300769.3641163.986
370.00180.00010.00320.0108-0.0048-0.0001-0.05470.0688-0.015-0.05950.0653-0.1028-0.00550.0636-0.00040.90890.1031-0.15260.7495-0.18780.6514-26.513273.1393162.7474
380.0353-0.03190.01210.08690.02870.02840.07220.04610.1131-0.02660.01770.0551-0.1425-0.01810.00410.28-0.09540.10960.4863-0.18090.2719-14.822564.9372166.1063
390.05510.03280.010.0549-0.00760.01270.02180.00850.252-0.0624-0.0853-0.1126-0.3002-0.15820.03380.38010.07780.12240.2692-0.08490.4022-20.827666.8439170.5519
400.0047-0.0020.00040.00130.0006-0.0022-0.03890.0416-0.06050.0033-0.0691-0.00120.0332-0.0070.00020.34810.2044-0.07150.9503-0.18780.7842-41.906375.2068174.6467
410.1362-0.1043-0.02890.120.01460.0018-0.17550.03460.0683-0.2185-0.03660.0740.0804-0.0871-0.01780.35620.0825-0.12590.1698-0.02860.3787-31.728662.1334168.339
420.0415-0.0160.03340.0374-0.01910.0330.0241-0.0068-0.0121-0.01850.0454-0.0006-0.0245-0.07530.06090.6411-0.1813-0.35420.5059-0.30520.6355-30.613651.7141167.2134
430.0009-0.00430.00080.01380.01680.0038-0.06110.1039-0.07970.0789-0.070.1155-0.1963-0.0842-0.00010.412-0.12430.02830.7356-0.05910.3221-34.985367.2053178.1423
440.0221-0.03830.04610.0193-0.07260.0633-0.0592-0.1486-0.31180.21080.0049-0.1119-0.2477-0.014800.3741-0.06790.09910.2606-0.03910.353919.39350.6217220.3658
450.2050.20250.05810.17230.04710.04640.12750.205-0.0153-0.28970.0897-0.40820.2674-0.03640.07390.4131-0.0748-0.02170.26190.03920.407829.876755.666226.2312
460.0361-0.00940.01610.0552-0.03590.0168-0.03350.079-0.0394-0.172-0.1519-0.0648-0.095-0.0482-0.08410.24380.0056-0.04170.69-0.07910.072621.781461.806215.7253
470.0312-0.0080.02320.083-0.04760.0567-0.444-0.06380.30930.2284-0.1501-0.18050.0677-0.1548-0.0130.33840.0094-0.010.3434-0.05520.335121.76764.8847227.0911
480.0241-0.0042-0.0340.0118-0.0050.0416-0.0342-0.01850.0953-0.17520.00620.0716-0.0462-0.10340.01220.5271-0.0569-0.04820.226-0.05410.476323.321957.2206230.4003
490.0904-0.04720.14180.17730.06750.3994-0.24410.1218-0.0424-0.2-0.613-0.05110.0498-0.0302-0.61340.1874-0.28670.08140.05780.36350.053516.496358.6005219.1436
500.2439-0.0843-0.00720.454-0.06930.20690.0256-0.0973-0.105-0.1567-0.0009-0.0123-0.0793-0.01270.23290.4073-0.0553-0.01790.15950.05930.26578.78150.5003206.1217
510.00250.0172-0.01280.0484-0.0115-0.0030.0552-0.0985-0.105-0.0830.17870.07690.03890.29520.00010.56170.0347-0.04590.34260.00760.48336.369840.4424202.6168
520.08320.00230.01890.02220.00310.02750.16610.16790.0421-0.22710.04750.1688-0.1183-0.17720.07820.4368-0.01050.00680.2154-0.07490.4844-0.087852.1636205.4936
530.01220.00180.0002-0.0074-0.00080.0156-0.3149-0.1277-0.0151-0.10080.16770.14070.17170.0759-0.00010.6644-0.03430.02440.2332-0.04160.53381.871435.3139194.9649
540.0085-0.0008-0.0080.0128-0.01980.02240.06650.00850.09660.1872-0.0240.15910.04220.06690.00010.4047-0.1502-0.03440.32260.07780.5025-7.215936.856203.1248
550.29270.08180.10830.21990.23520.14470.04180.3309-0.0164-0.00860.20340.1475-0.22160.09280.01690.5789-0.0252-0.02920.51830.06770.276129.626467.4029196.1755
560.3047-0.01690.04370.00920.1390.0444-0.06190.06820.1437-0.24660.18080.1657-0.18990.0898-0.00010.43620.0093-0.05030.34170.04130.243735.597267.4669206.8615
570.11850.0150.0779-0.02190.1110.20120.34320.1669-0.04940.1999-0.1224-0.19250.2880.315-0.0170.50250.0584-0.0380.2906-0.07640.321425.763357.5099193.1878
580.0501-0.0113-0.0560.382-0.43740.3798-0.1378-0.0610.140.11410.01360.0935-0.22430.28-0.09370.554-0.0581-0.03460.1135-0.04110.27322.34355.5691195.2664
590.11490.18770.01430.1939-0.01250.0948-0.0846-0.17850.0379-0.0734-0.1295-0.0062-0.14750.1507-0.0420.4252-0.050.05080.31210.07340.28928.699850.2215196.0436
600.0330.00730.0173-0.0111-0.06290.04160.2077-0.010.2657-0.2514-0.10230.1871-0.102-0.2546-00.4095-0.02260.03340.38850.03690.3893-1.34562.1645190.5642
610.21850.0981-0.05170.130.25960.45680.2338-0.1487-0.12260.0114-0.01340.0886-0.14760.18410.050.3970.00680.03520.29530.10930.329714.543258.8399182.5409
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 226 )
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 8 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 77 )
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 83 )
12X-RAY DIFFRACTION12chain 'B' and (resid 84 through 97 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 21 )
14X-RAY DIFFRACTION14chain 'C' and (resid 22 through 158 )
15X-RAY DIFFRACTION15chain 'C' and (resid 159 through 216 )
16X-RAY DIFFRACTION16chain 'C' and (resid 217 through 270 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 17 )
18X-RAY DIFFRACTION18chain 'D' and (resid 18 through 37 )
19X-RAY DIFFRACTION19chain 'D' and (resid 38 through 52 )
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 75 )
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 91 )
22X-RAY DIFFRACTION22chain 'D' and (resid 92 through 103 )
23X-RAY DIFFRACTION23chain 'D' and (resid 104 through 135 )
24X-RAY DIFFRACTION24chain 'D' and (resid 136 through 150 )
25X-RAY DIFFRACTION25chain 'D' and (resid 151 through 165 )
26X-RAY DIFFRACTION26chain 'D' and (resid 166 through 184 )
27X-RAY DIFFRACTION27chain 'D' and (resid 185 through 198 )
28X-RAY DIFFRACTION28chain 'E' and (resid 3 through 73 )
29X-RAY DIFFRACTION29chain 'E' and (resid 74 through 109 )
30X-RAY DIFFRACTION30chain 'E' and (resid 110 through 162 )
31X-RAY DIFFRACTION31chain 'E' and (resid 163 through 242 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 11 )
33X-RAY DIFFRACTION33chain 'F' and (resid 12 through 19 )
34X-RAY DIFFRACTION34chain 'F' and (resid 20 through 30 )
35X-RAY DIFFRACTION35chain 'F' and (resid 31 through 41 )
36X-RAY DIFFRACTION36chain 'F' and (resid 42 through 46 )
37X-RAY DIFFRACTION37chain 'F' and (resid 47 through 51 )
38X-RAY DIFFRACTION38chain 'F' and (resid 52 through 56 )
39X-RAY DIFFRACTION39chain 'F' and (resid 57 through 71 )
40X-RAY DIFFRACTION40chain 'F' and (resid 72 through 77 )
41X-RAY DIFFRACTION41chain 'F' and (resid 78 through 84 )
42X-RAY DIFFRACTION42chain 'F' and (resid 85 through 90 )
43X-RAY DIFFRACTION43chain 'F' and (resid 91 through 99 )
44X-RAY DIFFRACTION44chain 'G' and (resid 2 through 17 )
45X-RAY DIFFRACTION45chain 'G' and (resid 18 through 31 )
46X-RAY DIFFRACTION46chain 'G' and (resid 32 through 42 )
47X-RAY DIFFRACTION47chain 'G' and (resid 43 through 59 )
48X-RAY DIFFRACTION48chain 'G' and (resid 60 through 75 )
49X-RAY DIFFRACTION49chain 'G' and (resid 76 through 91 )
50X-RAY DIFFRACTION50chain 'G' and (resid 92 through 135 )
51X-RAY DIFFRACTION51chain 'G' and (resid 136 through 155 )
52X-RAY DIFFRACTION52chain 'G' and (resid 156 through 175 )
53X-RAY DIFFRACTION53chain 'G' and (resid 176 through 189 )
54X-RAY DIFFRACTION54chain 'G' and (resid 190 through 201 )
55X-RAY DIFFRACTION55chain 'H' and (resid 1 through 25 )
56X-RAY DIFFRACTION56chain 'H' and (resid 26 through 104 )
57X-RAY DIFFRACTION57chain 'H' and (resid 105 through 124 )
58X-RAY DIFFRACTION58chain 'H' and (resid 125 through 173 )
59X-RAY DIFFRACTION59chain 'H' and (resid 174 through 202 )
60X-RAY DIFFRACTION60chain 'H' and (resid 203 through 215 )
61X-RAY DIFFRACTION61chain 'H' and (resid 216 through 245 )

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万見について

-
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