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- PDB-5u6q: Structure of human MR1-3-F-SA in complex with human MAIT A-F7 TCR -

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基本情報

登録情報
データベース: PDB / ID: 5u6q
タイトルStructure of human MR1-3-F-SA in complex with human MAIT A-F7 TCR
要素
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
キーワードIMMUNE SYSTEM / T-cell receptor / MHC-like molecule
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 ferrous iron binding / positive regulation of transferrin 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 ferrous iron binding / positive regulation of transferrin 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
3-methanoyl-2-oxidanyl-benzoic acid / 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: 1.9 Å
データ登録者Keller, A.N. / 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)CE140100011 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)AF50 オーストラリア
引用ジャーナル: Nat. Immunol. / 年: 2017
タイトル: Drugs and drug-like molecules can modulate the function of mucosal-associated invariant T cells.
著者: Keller, A.N. / Eckle, S.B. / Xu, W. / Liu, L. / Hughes, V.A. / Mak, J.Y. / Meehan, B.S. / Pediongco, T. / Birkinshaw, R.W. / Chen, Z. / Wang, H. / D'Souza, C. / Kjer-Nielsen, L. / Gherardin, ...著者: Keller, A.N. / Eckle, S.B. / Xu, W. / Liu, L. / Hughes, V.A. / Mak, J.Y. / Meehan, B.S. / Pediongco, T. / Birkinshaw, R.W. / Chen, Z. / Wang, H. / D'Souza, C. / Kjer-Nielsen, L. / Gherardin, N.A. / Godfrey, D.I. / Kostenko, L. / Corbett, A.J. / Purcell, A.W. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J.
履歴
登録2016年12月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年2月8日Provider: repository / タイプ: Initial release
改定 1.12017年9月13日Group: Author supporting evidence / Data collection / カテゴリ: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
改定 1.22017年11月22日Group: Refinement description / カテゴリ: software
改定 1.32018年4月18日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.42020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.62024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: MAIT T-cell receptor alpha chain
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
A: Major histocompatibility complex class I-related gene protein
B: MAIT T-cell receptor alpha chain
G: MAIT T-cell receptor beta chain
H: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)187,87814
ポリマ－187,3138
非ポリマー5656
水25,7431429
1
C: Major histocompatibility complex class I-related gene protein
D: MAIT T-cell receptor alpha chain
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9747
ポリマ－93,6564
非ポリマー3173
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-45 kcal/mol
Surface area36720 Å2
手法PISA
2
A: Major histocompatibility complex class I-related gene protein
B: MAIT T-cell receptor alpha chain
G: MAIT T-cell receptor beta chain
H: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9057
ポリマ－93,6564
非ポリマー2483
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-48 kcal/mol
Surface area36230 Å2
手法PISA
単位格子
Length a, b, c (Å)217.668, 70.510, 143.370
Angle α, β, γ (deg.)90.000, 104.770, 90.000
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 2種, 4分子 CAFH

#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 / 断片: UNP residues 23-292 / 由来タイプ: 組換発現 / 詳細: Fragment: extracellular domain, residues 23-292 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MR1 / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q95460
#4: タンパク質 Beta-2-microglobulin


分子量: 11748.160 Da / 分子数: 2 / 断片: 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 / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P61769

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MAIT T-cell receptor ... , 2種, 4分子 DBEG

#2: タンパク質 MAIT T-cell receptor alpha chain


分子量: 22650.072 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: TRAV/TRAC / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
#3: タンパク質 MAIT T-cell receptor beta chain


分子量: 27546.562 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: TRBV/TRBC / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)

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非ポリマー , 5種, 1435分子

#5: 化合物 ChemComp-7ZS / 3-methanoyl-2-oxidanyl-benzoic acid / 3-ホルミルサリチル酸


分子量: 166.131 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H6O4
#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: 1 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: 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: 1 / 由来タイプ: 合成 / 式: Na
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1429 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.84 Å3/Da / 溶媒含有率: 56.69 % / Mosaicity: 0.57 °
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: BTP, PEG 3350, NaAc

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データ収集

回折平均測定温度: 100 K
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: 0.953 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年10月20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: 0.953 Å / 相対比: 1
反射解像度: 1.9→44.386 Å / Num. obs: 161424 / % possible obs: 97.6 % / 冗長度: 4.5 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.045 / Rrim(I) all: 0.097 / Net I/σ(I): 11.1 / Num. measured all: 722223 / Scaling rejects: 100
反射 シェル解像度: 1.9→1.93 Å / 冗長度: 4.6 % / Rmerge(I) obs: 0.746 / Num. unique all: 7648 / CC1/2: 0.746 / % possible all: 94.2

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
MOSFLMデータ削減
Aimless0.3.11データスケーリング
PHASER位相決定
PDB_EXTRACT3.2データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 4L4T

4l4t


解像度: 1.9→44.386 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.53
Rfactor反射数%反射
Rfree0.222 8114 5.03 %
Rwork0.1818 --
obs0.1838 161369 97.4 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 119.09 Å2 / Biso mean: 36.2564 Å2 / Biso min: 13.24 Å2
精密化ステップサイクル: final / 解像度: 1.9→44.386 Å
タンパク質核酸リガンド溶媒全体
原子数12799 0 37 1429 14265
Biso mean--32.76 39.56 -
残基数----1598
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00913254
X-RAY DIFFRACTIONf_angle_d1.18818029
X-RAY DIFFRACTIONf_chiral_restr0.1781898
X-RAY DIFFRACTIONf_plane_restr0.0062360
X-RAY DIFFRACTIONf_dihedral_angle_d18.864807
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.33932730.29364882515594
1.9216-1.94420.38142620.30564909517194
1.9442-1.96790.29772480.26324927517594
1.9679-1.99280.29152300.24284947517794
1.9928-2.0190.27962730.23644911518494
2.019-2.04670.27032760.22774963523995
2.0467-2.07590.23952360.21295065530195
2.0759-2.10690.26762620.20694963522596
2.1069-2.13990.25822790.20425023530296
2.1399-2.17490.2462760.19915012528897
2.1749-2.21240.22993040.20065052535697
2.2124-2.25270.30252570.23445099535698
2.2527-2.2960.28922550.21215132538798
2.296-2.34290.2382820.20065122540498
2.3429-2.39380.22082880.19265097538598
2.3938-2.44950.24182520.18815144539698
2.4495-2.51070.23582880.19295121540998
2.5107-2.57860.26072700.18485169543998
2.5786-2.65450.24332510.18675203545499
2.6545-2.74010.23422560.18365161541799
2.7401-2.83810.21712750.18965183545899
2.8381-2.95170.25553050.19425183548899
2.9517-3.0860.22772880.18625156544499
3.086-3.24860.21562590.17375218547799
3.2486-3.45210.2052550.17055243549899
3.4521-3.71850.19192850.15785232551799
3.7185-4.09250.18212550.15625264551999
4.0925-4.68410.16612900.13175223551399
4.6841-5.89930.1813140.14845269558399
5.8993-44.39810.20342700.1755382565298
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.40660.16870.00641.339-0.74971.5864-0.0257-0.10980.23570.08040.1360.1232-0.0042-0.1976-0.10550.1160.0406-0.01150.21970.00070.2328-49.514943.6491192.132
21.69230.08380.17031.0849-0.27910.88850.00070.07130.1223-0.0220.093-0.06440.05-0.0622-0.09620.13120.0042-0.01090.1360.00370.1712-41.803342.3407180.8829
31.5348-0.77410.58661.26310.27432.4882-0.06730.32780.5197-0.2621-0.0207-0.0954-0.39410.11980.08050.2884-0.1311-0.0790.52960.21040.4109-67.884746.3756160.5065
43.4201-0.7769-0.64972.4401-0.11871.99650.1291-0.0612-0.34650.0657-0.01040.1510.1213-0.1613-0.10610.23870.02630.02030.1086-0.03060.2045-23.435715.6885196.637
52.4469-1.15711.34890.5682-0.51171.04270.04590.2066-0.2685-0.1446-0.0239-0.0450.0239-0.0044-0.0340.24360.0258-0.00080.1436-0.05220.2417-19.43618.7246191.0427
62.3163-0.74781.9971.3394-0.83923.5477-0.0646-0.08090.13530.04890.1072-0.05790.03780.0383-0.02090.17190.04340.00430.1339-0.04630.1943-25.211628.7206194.8988
77.2680.01033.17810.9832-0.6433.00660.06890.47720.0646-0.2047-0.0325-0.10490.04560.2625-0.04330.26130.04330.04580.1401-0.0340.2193-20.660725.0962186.1267
83.7491-0.82620.63510.962-0.34821.2362-0.08020.0465-0.0766-0.02870.0793-0.06580.0066-0.0506-0.00060.20530.0423-0.00180.1312-0.04090.1629-21.968724.047197.2571
91.5974-0.6157-0.14360.74521.03751.86420.01820.046-0.05060.2162-0.0192-0.00660.1260.0986-0.03360.26190.01380.02060.096-0.01510.223.53811.8902217.3981
103.10251.1034-0.72413.0115-1.72656.20220.0380.2687-0.44780.1683-0.08450.1810.687-0.81540.09960.3699-0.02930.03730.2348-0.10540.3624-4.8265.7453211.5817
115.36032.042-2.09245.0679-2.68746.69590.00430.72550.3315-0.13950.13260.1865-0.198-0.2823-0.08750.19320.05870.02910.1785-0.04260.1962-1.326517.9386211.1627
122.4948-0.509-0.40750.87011.12451.4807-0.1352-0.0486-0.46270.34730.01640.08250.5993-0.20890.17090.36880.01080.06140.1056-0.02140.2855-0.70167.6951219.4142
137.61682.11221.08724.53741.47043.3470.20620.4316-0.71830.3786-0.1724-0.080.72130.0192-0.00540.37230.03040.04380.18-0.0790.3364.53781.9587212.655
141.6787-0.57180.30451.5874-0.77511.9393-0.1451-0.33960.2050.16010.0536-0.0511-0.1984-0.14160.08240.19080.0888-0.0240.2445-0.07360.1835-33.479834.0024212.3803
151.1713-0.28840.01522.3166-1.58312.0723-0.1672-0.25980.10370.07530.220.0871-0.1261-0.4191-0.03440.16770.0761-0.03360.2488-0.0690.1937-31.877732.7436209.5824
164.3468-0.67221.49141.38-0.37442.86190.1799-0.0948-0.3005-0.0361-0.09690.16640.1819-0.6154-0.02880.20350.00310.00450.2627-0.03850.1944-25.936319.7873227.977
172.5967-0.0485-0.73030.90390.63251.48440.09260.16850.07220.0088-0.0865-0.0284-0.1609-0.1215-0.00540.21990.05210.00910.1261-0.00250.183-1.671619.7672221.744
182.4588-0.6123-0.57292.67460.21393.5530.11680.6397-0.1206-0.0235-0.08230.28220.0114-0.58670.01880.24430.0984-0.02680.2229-0.0430.1754-11.274418.528219.6589
191.80870.1279-1.76680.2615-0.47072.11290.12040.28790.2429-0.0196-0.0371-0.023-0.2225-0.1343-0.07680.25940.04810.00890.0855-0.02940.20391.761921.1307218.5114
207.54120.4911-0.61770.0979-0.30851.11110.1435-0.18120.55760.15840.0609-0.1451-0.3611-0.0538-0.17210.36560.05510.02360.142-0.06070.30351.758828.028225.5948
214.05181.4793-1.08790.7533-0.36892.12150.10610.0351-0.1180.01-0.0655-0.0053-0.0781-0.1861-0.07910.25230.0693-0.030.1896-0.04770.2146-14.927625.144233.667
222.74260.74250.222.14690.23751.7612-0.02780.07230.4382-0.2695-0.0340.1351-0.1783-0.27740.02610.23810.0306-0.07960.37210.13850.5221-62.060958.0934177.5807
232.2103-0.4236-1.06780.91920.6140.7188-0.04050.019-0.284-0.0525-0.35560.9631-0.0332-0.9070.23410.2815-0.0226-0.17450.81010.12530.8263-81.947446.4387175.281
241.8622-0.63140.08460.25150.05820.2358-0.03070.04250.2950.07080.31060.5564-0.2392-0.6459-0.07630.11770.0285-0.06870.60230.1440.5999-69.409351.5999180.3417
252.2402-0.96011.11830.7315-0.10171.083-0.0219-0.74310.84480.11440.03410.3646-0.2049-0.6463-0.020.29330.1004-0.01740.4835-0.03850.6472-65.177659.2173186.8296
260.50340.6050.91762.6523-0.70233.8031-0.0861-0.26840.46620.17220.10850.0998-0.4766-0.4368-0.00820.23760.3237-0.0920.8731-0.19651.3383-79.149260.9429188.024
272.3134-2.8429-2.31855.67130.54334.78160.2006-0.63340.35780.71120.11150.6528-0.0369-0.651-0.18750.29530.0250.0340.66990.04120.6166-73.17551.3424191.2972
288.57251.7924-3.62911.7669-1.41413.00480.1007-0.04580.1116-0.03220.14920.2357-0.0086-0.2236-0.19450.1790.0235-0.03420.24420.04930.326-54.151849.8167182.5664
298.7311-0.49330.59250.34260.32260.6666-0.0961-0.21840.37030.07420.06580.51320.0498-0.56490.03280.19450.0416-0.02520.50520.06460.4471-69.994450.3758183.9568
307.803-1.4513-1.70294.37412.72351.7801-0.26510.64590.3755-0.77590.05120.4676-0.4107-0.0780.12270.39390.2015-0.2691.19020.05591.0951-86.155857.3352177.6174
313.39030.10071.12890.01460.01091.13310.1407-0.21150.7590.0023-0.10420.6373-0.4244-0.5276-0.03340.31430.1559-0.04820.4913-0.03510.8921-66.354664.2084183.7625
321.16560.1263-1.94625.7514-0.99943.3747-0.27030.15840.7818-0.41240.16250.0433-0.226-0.70320.03080.40060.2356-0.21990.67740.04410.82-75.185160.0079175.7454
330.8701-0.1397-0.10691.98680.11521.3590.0625-0.17420.02310.0041-0.1788-0.1768-0.10530.05710.11410.16570.01820.01170.25090.05380.17384.82129.2203255.2048
341.2897-0.145-0.27382.18910.67960.85390.0694-0.0336-0.015-0.239-0.2368-0.0696-0.0075-0.14510.16030.19620.05840.02140.2590.04230.1384-2.918422.1593245.0641
351.8556-0.2737-01.4727-0.21580.95360.04030.1521-0.1132-0.062-0.0194-0.1762-0.03070.0479-0.0310.2908-0.01710.04320.10280.01050.275820.75338.3391224.8625
362.52960.1244-0.21670.9116-0.02631.2005-0.0712-0.04060.0429-0.03590.01890.07460.0237-0.11450.05420.20330.0656-0.0210.3853-0.0940.1726-27.967728.6609256.1708
373.1612-1.48-1.00971.8144-0.29510.8113-0.10720.4878-0.6787-0.13140.26850.57890.2041-0.7152-0.12370.2509-0.0249-0.03510.8613-0.07740.3896-50.521225.6022264.2981
384.7940.42531.27412.35470.09755.66870.12660.21520.39580.04630.1970.27690.2281-0.4383-0.24760.27660.02640.02110.5982-0.02060.4441-53.121627.3941277.2318
390.91190.85041.5112.47570.22893.4999-0.2736-0.53841.0917-0.01460.50830.6754-0.2871-1.0565-0.21890.40490.1414-0.00611.1111-0.20941.0451-61.769434.0613279.2119
403.6278-1.0543-1.52731.3105-0.30061.2056-0.017-0.6107-0.23490.3759-0.38320.33880.2444-0.51520.39690.29280.05820.04110.5557-0.08160.2133-20.839424.5842282.9006
412.1796-0.1818-0.69891.07180.59171.8314-0.1542-0.3290.06110.217-0.07880.0311-0.00970.04030.22640.25340.0817-0.00940.3996-0.05250.162-12.080228.5135274.0379
421.9925-1.4514-1.71883.64632.01862.45850.0363-0.38460.31350.1054-0.0428-0.1475-0.17970.1281-0.00660.29430.08-0.0040.5734-0.10690.2085-16.257931.599279.0511
432.4547-0.56051.86973.22850.84891.9424-0.13980.4813-0.2558-0.2898-0.2011-0.2249-0.1704-0.13080.38280.30260.07480.02610.4286-0.05310.2438-14.925721.9675263.4986
442.4928-0.1492-1.93140.4206-0.50732.42770.1253-0.24080.52880.18550.3572-0.1481-0.06670.2264-0.39490.36070.08750.02490.593-0.18980.3187-28.29833.9807291.1734
453.57250.391.99031.82760.27752.57850.38990.0295-0.58960.03640.18410.09340.6455-0.1355-0.51780.4359-0.0202-0.05110.4739-0.0320.3291-46.009722.1746283.8387
466.0520.40470.4134.88080.94537.3415-0.0387-0.94070.05620.75430.1853-0.7049-0.20970.6466-0.20510.6470.1202-0.03330.7614-0.06630.3287-26.985528.3577298.9606
475.01482.20450.53762.02260.45181.13570.4713-0.2509-0.75360.03410.33310.56750.9886-0.8572-0.66960.8504-0.2123-0.20290.89230.31040.6206-47.681614.7734291.8821
482.03110.5623-0.06852.3465-0.01192.0495-0.0366-0.1315-0.25240.0958-0.0754-0.0045-0.01850.13110.0710.1917-0.00230.01180.15130.04670.249424.095324.7925241.4008
492.81260.54771.38911.0704-0.23951.4291-0.27880.09650.60950.1791-0.2162-0.5284-0.85540.88860.30330.5997-0.2081-0.08390.29690.0850.510332.724945.9173237.1543
502.20260.9334-0.14483.7886-0.66171.9519-0.2522-0.16390.1146-0.01510.1939-0.2701-0.29710.15750.05810.2584-0.0215-0.03190.18920.01330.269725.731834.773243.2214
518.10485.4633-0.39315.5373-0.40261.90320.1396-0.6341-0.31980.6536-0.1486-0.3837-0.12850.16850.01590.3281-0.0006-0.08070.32760.09250.316926.987626.6667250.7689
525.61541.338-0.65182.21810.06862.9162-0.0917-1.02350.11690.83460.0459-0.6951-0.66440.56490.07180.5898-0.0694-0.1820.54380.01970.445433.051236.5674253.0414
534.8825.08291.47979.09474.23113.8193-0.2224-0.2270.007-0.00910.3220.0608-0.14450.0720.02170.21940.04250.03930.2410.08810.224512.670326.5226246.0396
546.39073.7998-0.16134.9453-0.51312.5003-0.0513-0.27240.41670.19020.03330.0015-0.55860.15690.09190.3423-0.0284-0.03040.24160.0080.256525.335336.4058246.712
554.60711.3824-0.26925.1566-2.07963.13630.110.17390.3463-0.4037-0.2038-0.63580.11750.61540.15880.4786-0.1253-0.16930.59430.12040.859842.722839.7799240.9323
563.41451.9888-0.14466.2684-1.03062.7244-0.1198-0.3374-0.2330.62-0.112-0.5643-0.04050.35260.19980.24930.0329-0.030.27820.11170.330631.333523.0864248.2504
573.45770.01770.36867.4568-2.80154.6701-0.02520.13330.4108-0.4568-0.0522-0.4041-0.36910.67440.07180.2556-0.05720.00180.37370.11350.466935.596832.3112238.1303
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 0 through 84 )C0 - 84
2X-RAY DIFFRACTION2chain 'C' and (resid 85 through 182 )C85 - 182
3X-RAY DIFFRACTION3chain 'C' and (resid 183 through 269 )C183 - 269
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 13 )D1 - 13
5X-RAY DIFFRACTION5chain 'D' and (resid 14 through 25 )D14 - 25
6X-RAY DIFFRACTION6chain 'D' and (resid 26 through 52 )D26 - 52
7X-RAY DIFFRACTION7chain 'D' and (resid 53 through 75 )D53 - 75
8X-RAY DIFFRACTION8chain 'D' and (resid 76 through 108 )D76 - 108
9X-RAY DIFFRACTION9chain 'D' and (resid 109 through 135 )D109 - 135
10X-RAY DIFFRACTION10chain 'D' and (resid 136 through 150 )D136 - 150
11X-RAY DIFFRACTION11chain 'D' and (resid 151 through 165 )D151 - 165
12X-RAY DIFFRACTION12chain 'D' and (resid 166 through 185 )D166 - 185
13X-RAY DIFFRACTION13chain 'D' and (resid 186 through 200 )D186 - 200
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 73 )E1 - 73
15X-RAY DIFFRACTION15chain 'E' and (resid 74 through 109 )E74 - 109
16X-RAY DIFFRACTION16chain 'E' and (resid 110 through 124 )E110 - 124
17X-RAY DIFFRACTION17chain 'E' and (resid 125 through 162 )E125 - 162
18X-RAY DIFFRACTION18chain 'E' and (resid 163 through 188 )E163 - 188
19X-RAY DIFFRACTION19chain 'E' and (resid 189 through 202 )E189 - 202
20X-RAY DIFFRACTION20chain 'E' and (resid 203 through 215 )E203 - 215
21X-RAY DIFFRACTION21chain 'E' and (resid 216 through 244 )E216 - 244
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 11 )F1 - 11
23X-RAY DIFFRACTION23chain 'F' and (resid 12 through 19 )F12 - 19
24X-RAY DIFFRACTION24chain 'F' and (resid 20 through 30 )F20 - 30
25X-RAY DIFFRACTION25chain 'F' and (resid 31 through 41 )F31 - 41
26X-RAY DIFFRACTION26chain 'F' and (resid 42 through 46 )F42 - 46
27X-RAY DIFFRACTION27chain 'F' and (resid 47 through 51 )F47 - 51
28X-RAY DIFFRACTION28chain 'F' and (resid 52 through 61 )F52 - 61
29X-RAY DIFFRACTION29chain 'F' and (resid 62 through 71 )F62 - 71
30X-RAY DIFFRACTION30chain 'F' and (resid 72 through 77 )F72 - 77
31X-RAY DIFFRACTION31chain 'F' and (resid 78 through 90 )F78 - 90
32X-RAY DIFFRACTION32chain 'F' and (resid 91 through 97 )F91 - 97
33X-RAY DIFFRACTION33chain 'A' and (resid 0 through 84 )A0 - 84
34X-RAY DIFFRACTION34chain 'A' and (resid 85 through 171 )A85 - 171
35X-RAY DIFFRACTION35chain 'A' and (resid 172 through 270 )A172 - 270
36X-RAY DIFFRACTION36chain 'B' and (resid 2 through 102 )B2 - 102
37X-RAY DIFFRACTION37chain 'B' and (resid 103 through 116 )B103 - 116
38X-RAY DIFFRACTION38chain 'B' and (resid 117 through 175 )B117 - 175
39X-RAY DIFFRACTION39chain 'B' and (resid 176 through 200 )B176 - 200
40X-RAY DIFFRACTION40chain 'G' and (resid 2 through 14 )G2 - 14
41X-RAY DIFFRACTION41chain 'G' and (resid 15 through 73 )G15 - 73
42X-RAY DIFFRACTION42chain 'G' and (resid 74 through 94 )G74 - 94
43X-RAY DIFFRACTION43chain 'G' and (resid 95 through 109 )G95 - 109
44X-RAY DIFFRACTION44chain 'G' and (resid 110 through 124 )G110 - 124
45X-RAY DIFFRACTION45chain 'G' and (resid 125 through 215 )G125 - 215
46X-RAY DIFFRACTION46chain 'G' and (resid 216 through 233 )G216 - 233
47X-RAY DIFFRACTION47chain 'G' and (resid 234 through 244 )G234 - 244
48X-RAY DIFFRACTION48chain 'H' and (resid 1 through 11 )H1 - 11
49X-RAY DIFFRACTION49chain 'H' and (resid 12 through 19 )H12 - 19
50X-RAY DIFFRACTION50chain 'H' and (resid 20 through 30 )H20 - 30
51X-RAY DIFFRACTION51chain 'H' and (resid 31 through 41 )H31 - 41
52X-RAY DIFFRACTION52chain 'H' and (resid 42 through 51 )H42 - 51
53X-RAY DIFFRACTION53chain 'H' and (resid 52 through 61 )H52 - 61
54X-RAY DIFFRACTION54chain 'H' and (resid 62 through 71 )H62 - 71
55X-RAY DIFFRACTION55chain 'H' and (resid 72 through 77 )H72 - 77
56X-RAY DIFFRACTION56chain 'H' and (resid 78 through 90 )H78 - 90
57X-RAY DIFFRACTION57chain 'H' and (resid 91 through 99 )H91 - 99

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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