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- PDB-5u16: Structure of human MR1-2-OH-1-NA 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: 5u16
タイトルStructure of human MR1-2-OH-1-NA 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
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-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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
2-hydroxynaphthalene-1-carbaldehyde / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2 Å
データ登録者Keller, A.N. / Birkinshaw, R.W. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC)CE140100011 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11月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年2月15日Provider: repository / タイプ: Initial release
改定 1.12018年4月18日Group: Data collection / Database references / カテゴリ: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
改定 1.22020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.42024年10月16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
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: MAIT T-cell receptor beta chain
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,29321
ポリマ－187,3138
非ポリマー98013
水21,9241217
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,10710
ポリマ－93,6564
非ポリマー4506
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-74 kcal/mol
Surface area37050 Å2
手法PISA
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: MAIT T-cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,18611
ポリマ－93,6564
非ポリマー5307
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-72 kcal/mol
Surface area36070 Å2
手法PISA
単位格子
Length a, b, c (Å)216.440, 69.850, 143.120
Angle α, β, γ (deg.)90.000, 104.350, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain C
12chain B
22chain D
13chain E
23chain G
14chain F
24chain H

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALchain AAA0 - 2691 - 270
21ARGARGVALVALchain CCC1 - 2692 - 270
12ILEILEASPASPchain BBB1 - 961 - 96
22ILEILEMETMETchain DDD1 - 991 - 99
13GLYGLYPROPROchain EEE1 - 1981 - 198
23GLYGLYPROPROchain GGG1 - 2001 - 200
14GLYGLYGLYGLYchain FFF3 - 2423 - 242
24ASNASNARGARGchain HHH1 - 2431 - 243

NCSアンサンブル:
ID
1
2
3
4

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要素

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タンパク質 , 2種, 4分子 ACBD

#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: Residue K43 is covalently bound to the compound 2-hydroxy-1-napthaldehyde through a Schiff-base bond.
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
#2: 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 EGFH

#3: 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)
#4: 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, 1230分子

#5: 化合物 ChemComp-7WO / 2-hydroxynaphthalene-1-carbaldehyde / 2-ヒドロキシ-1-ナフトアルデヒド


分子量: 172.180 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C11H8O2
#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Cl
#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: 3 / 由来タイプ: 合成 / 式: Na
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1217 / 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: 2.8 Å3/Da / 溶媒含有率: 56.04 %
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: 2015年3月22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: 2→69.327 Å / Num. obs: 139855 / % possible obs: 99.8 % / 冗長度: 3.7 % / Net I/σ(I): 1.3
反射 シェル解像度: 2→2.03 Å / 冗長度: 3.7 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.66 / % possible all: 99.9

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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
MOSFLMデータ削減
Aimlessデータスケーリング
PHASER位相決定
PHENIX1.9_1692精密化
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: 2→69.327 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.18
Rfactor反射数%反射
Rfree0.2191 6975 4.99 %
Rwork0.173 --
obs0.1754 139754 99.72 %
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: 105.87 Å2 / Biso mean: 34.3862 Å2 / Biso min: 10.71 Å2
精密化ステップサイクル: final / 解像度: 2→69.327 Å
タンパク質核酸リガンド溶媒全体
原子数12776 0 60 1217 14053
Biso mean--33.39 36.79 -
残基数----1593
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0113217
X-RAY DIFFRACTIONf_angle_d1.22117927
X-RAY DIFFRACTIONf_chiral_restr0.0561892
X-RAY DIFFRACTIONf_plane_restr0.0072348
X-RAY DIFFRACTIONf_dihedral_angle_d13.9284772
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2399X-RAY DIFFRACTION8.863TORSIONAL
12C2399X-RAY DIFFRACTION8.863TORSIONAL
21B922X-RAY DIFFRACTION8.863TORSIONAL
22D922X-RAY DIFFRACTION8.863TORSIONAL
31E1604X-RAY DIFFRACTION8.863TORSIONAL
32G1604X-RAY DIFFRACTION8.863TORSIONAL
41F2181X-RAY DIFFRACTION8.863TORSIONAL
42H2181X-RAY DIFFRACTION8.863TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.31552460.282143464592100
2.0227-2.04650.31052390.282544104649100
2.0465-2.07150.31422220.257544094631100
2.0715-2.09770.28962190.247243954614100
2.0977-2.12530.29852370.232343844621100
2.1253-2.15440.29112000.231644524652100
2.1544-2.18520.24052460.21544724718100
2.1852-2.21780.2692200.20343324552100
2.2178-2.25250.24532410.201944374678100
2.2525-2.28940.26592440.20543474591100
2.2894-2.32890.25032410.207544764717100
2.3289-2.37130.2632290.201243774606100
2.3713-2.41690.28022360.197644234659100
2.4169-2.46620.24522120.192544404652100
2.4662-2.51980.22722280.186843974625100
2.5198-2.57840.23632450.178944184663100
2.5784-2.64290.2062310.174344054636100
2.6429-2.71440.22662270.175644044631100
2.7144-2.79430.2562390.189544344673100
2.7943-2.88450.24312560.18143524608100
2.8845-2.98760.23862190.16744644683100
2.9876-3.10720.20172330.163843764609100
3.1072-3.24860.19822230.160444534676100
3.2486-3.41990.21082260.15284424465099
3.4199-3.63410.18222500.146544394689100
3.6341-3.91470.19462280.148244434671100
3.9147-4.30860.17692360.13444440467699
4.3086-4.93190.14662250.118344974722100
4.9319-6.2130.17062320.141645174749100
6.213-69.3690.21122450.17284616486199
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)
11.6044-0.18340.03321.48080.67371.73470.02550.14020.1945-0.10610.0604-0.09930.01570.193-0.06660.1015-0.04640.00520.17210.00310.1733-5.040638.599516.0664
21.6864-0.0852-0.34284.3253-0.30021.0138-0.0022-0.07940.21040.125-0.02160.1297-0.0842-0.08210.0280.1096-0.0205-0.00530.1186-0.00470.1585-17.307841.745626.8358
35.44610.72513.54411.69410.42172.68110.22890.2203-0.4408-0.00190.1756-0.16220.33760.3846-0.43640.18760.0484-0.04140.2205-0.04920.17840.397424.541728.4365
41.33250.73550.08951.5999-0.26893.3676-0.0185-0.3770.49010.3692-0.0538-0.0785-0.5588-0.15880.06940.31570.1469-0.13230.5209-0.22460.425813.611841.616948.063
53.1769-2.96412.02433.46-2.67382.2359-0.2777-0.0920.81470.5350.1631-0.5584-0.39430.29170.17030.2709-0.0484-0.07540.3814-0.150.49427.650352.883530.6534
60.8346-0.15620.1491.67681.1280.8357-0.3733-0.2716-0.30050.222-0.1721-0.6671-0.02250.9624-0.1720.16460.0721-0.25370.7812-0.02740.912927.88240.692933.2357
72.41670.7374-0.15530.2763-0.18030.4197-0.0775-0.02990.0898-0.04380.2788-0.5858-0.06020.5307-0.04530.1653-0.0587-0.0830.4993-0.08390.573414.955246.283627.9049
84.30760.8509-0.58910.1861-0.09790.0809-0.22120.6060.4916-0.09010.0571-0.4192-0.35990.56570.02150.2137-0.1926-0.01060.49590.03720.566710.930853.984421.3552
92.08731.8385-2.12497.17561.36914.0506-0.01310.39940.5563-0.2230.26380.1439-0.43260.5356-0.16820.095-0.2354-0.02110.84110.19021.035124.926955.231520.1571
106.84823.1323-3.21682.10110.54468.3319-0.14590.6049-0.3038-0.7644-0.0609-1.12860.39270.49390.21210.293-0.0750.0830.7617-0.10580.640218.288345.279417.4229
119.593-4.019-6.54786.67713.08344.59560.0981-0.0310.2181-0.16110.2547-0.00460.1390.3545-0.3330.144-0.0295-0.03190.1937-0.01590.1769-0.329144.758425.6383
124.34021.2642-1.53690.9326-0.83270.8476-0.22440.74840.1405-0.09820.1571-0.58150.05720.57380.10180.1571-0.01450.03040.5353-0.10850.442415.534845.056524.239
131.65990.90590.12692.09090.72380.48630.1474-0.15150.17810.1530.0353-0.2726-0.10210.18220.24270.1011-0.1809-0.31291.1326-0.15591.220832.304252.023630.3507
140.60460.38780.75070.24720.47071.0467-0.07390.13350.9811-0.10270.0424-0.4943-0.74360.6023-0.09070.3541-0.1985-0.02510.45030.11570.987412.168259.310424.5203
152.98570.2114-2.20773.00720.55371.803-0.0344-0.27850.27630.6501-0.04780.1717-0.38260.673-0.03970.3585-0.1515-0.21940.5262-0.14560.82119.717855.47831.6939
161.15750.23190.00122.87410.10071.5415-0.00190.31140.062-0.1697-0.12190.279-0.0434-0.10070.10980.1381-0.0032-0.00670.3038-0.04240.1688-59.6823.9418-47.8806
171.19980.0294-0.12531.7901-0.70021.06380.09150.059-0.06120.1454-0.24840.0420.02340.07880.13840.1572-0.04220.00570.2316-0.0480.1263-51.723116.9823-37.2699
184.30263.4733-3.24453.6467-2.8253.7870.00540.0731-0.05680.0442-0.02580.1223-0.1218-0.11870.01570.22720.01860.01470.0771-0.03310.2183-75.584834.9364-18.9849
192.6376-0.13010.56333.51380.37572.98660.0048-0.3134-0.22270.3519-0.05480.15580.1943-0.27150.00660.22680.01830.03630.06980.01130.2501-75.17631.5743-14.655
204.2023-1.71340.34057.1309-0.7113.7567-0.01160.3607-0.06480.0956-0.1079-0.2348-0.01460.17510.11770.0993-0.0309-0.01390.1368-0.02870.1292-78.742620.1228-33.6674
211.5139-1.46751.43191.4273-1.38641.3496-0.0548-0.16660.9924-0.2046-0.15810.455-0.9769-0.6241-0.00620.37270.114-0.02720.2571-0.12220.5877-87.269641.7445-29.4243
224.2376-3.123-0.38414.57170.21332.17230.00750.59010.1198-0.5128-0.13250.2107-0.2718-0.02510.08310.21670.0016-0.05280.2087-0.04150.2281-80.872326.0783-39.3702
234.84471.7455-3.70156.8550.4523.4383-0.08551.2421-0.2458-0.94260.04030.9647-0.4969-1.16620.05430.37060.0393-0.19050.48140.06160.4317-93.099829.9665-44.4114
244.6709-5.67243.37947.4454-2.72925.9579-0.37011.62651.1671-0.90160.26150.3423-1.4895-0.56350.13530.62380.0566-0.16340.54580.13160.5063-82.343334.2562-46.4315
258.281-5.7262.28565.5299-3.76134.0116-0.29020.22650.20550.23190.2689-0.141-0.33940.33750.11550.2285-0.03140.00690.2345-0.11890.2353-67.326821.6679-38.2385
266.0129-6.7423-2.43157.8412.20544.23080.23040.73630.4129-0.5888-0.2625-0.0574-0.5449-0.0703-0.0130.2741-0.0299-0.04180.2089-0.01960.2797-79.773831.745-39.0737
272.39931.6664-2.77628.83813.85038.25050.22640.11890.57360.1528-0.44271.2278-0.3719-1.37550.16640.34130.1504-0.05160.5308-0.08250.7631-97.537335.7026-33.6782
281.52591.66490.6522.49752.19253.4007-0.01430.578-0.3731-0.6236-0.17240.7662-0.0596-0.19150.11360.2176-0.0476-0.07450.2782-0.0950.3472-85.970618.5504-40.6541
297.49752.07022.14874.66134.73468.16010.0861-0.75690.5570.4658-0.09930.6852-0.1394-0.54590.13270.2425-0.0020.01030.2796-0.06160.3417-90.127727.8365-30.4828
304.7362-2.6874-0.55315.2214-0.85843.1613-0.0305-0.09690.06130.0040.06930.0061-0.16480.2753-0.04590.1708-0.1069-0.02850.42320.0980.1579-19.436627.9287-50.9539
313.41-0.2686-1.5340.48890.14032.157-0.08610.08510.24550.03720.0377-0.0782-0.01770.03580.05260.171-0.0484-0.0310.27970.08190.1504-29.766326.1484-47.8371
324.6059-0.6211-2.93692.4913-1.02516.3118-0.18780.1292-0.1684-0.1384-0.0074-0.0490.12880.16690.12410.1548-0.0991-0.0350.27820.06010.154-29.545518.3137-51.4492
336.8474-5.5042-6.186.85595.93777.238-0.2383-0.3863-0.38380.3980.05450.00380.37070.2630.15650.2168-0.0415-0.03410.33030.0890.1643-24.819717.0907-42.0449
347.3685-1.8869-4.2243.06540.71514.9090.1917-0.23530.55870.32690.1245-0.3797-0.22930.6413-0.26550.2146-0.09720.01980.25550.07030.1333-26.80925.9768-40.7799
353.1731-0.9958-2.61751.26061.47494.0186-0.3178-0.1635-0.03840.10480.2593-0.17590.29830.35980.07610.2094-0.0649-0.00980.37920.07860.1671-20.676219.041-52.3192
364.4207-1.1603-3.81770.40421.51186.03430.27140.69680.3337-0.1211-0.14020.0793-0.1-0.6218-0.08220.2325-0.0489-0.02990.40090.13780.2093-38.687128.5414-51.881
376.67050.0026-2.66520.95091.16732.5336-0.1399-0.5547-0.48370.02630.3419-0.25910.49110.8799-0.15410.26410.049-0.01370.70980.05830.282-4.241420.1448-56.6606
387.9059-0.0562-1.22826.51441.22239.53970.0306-0.0403-0.2769-0.1531-0.0802-0.3802-0.21681.04670.00810.2353-00.00350.527-0.02660.38352.629721.1088-70.4605
395.47151.06994.04819.6115-1.25859.4142-0.22130.01541.02420.3290.66230.1433-1.202-0.3018-0.39810.35570.03980.08910.5681-0.00860.5205-4.442630.4429-70.1461
407.1322-0.48490.11055.3622-0.07427.91290.0144-0.3854-0.22780.10020.254-0.65180.23440.6328-0.1240.249-0.0587-0.04680.43590.00680.3382-1.116119.6779-68.195
416.24812.9613.61044.8908-1.6558.5003-0.1655-0.20891.02880.528-0.372-0.6221-0.43020.98630.5110.3924-0.13120.080.6511-0.09850.76428.619127.1147-65.6655
421.3133-0.2979-0.3441.6056-0.58523.44180.01350.3665-0.0276-0.2056-0.11930.0112-0.0511-0.19890.08720.2625-0.052-0.03160.44560.05320.1697-41.032722.3954-67.9649
432.37-1.12380.92514.1213-0.81622.6679-0.150.2310.1345-0.19710.07790.16780.0266-0.53450.01210.2237-0.0778-0.04140.41540.04120.1634-38.868422.0311-65.1243
447.5090.3018-4.49321.18671.61265.4480.57580.26550.614-0.36820.0760.1573-0.53510.0416-0.52680.40330.02350.06670.52020.12280.262-26.32928.0862-83.5683
454.47440.12452.03771.9359-0.22023.56250.48190.4596-0.8392-0.20460.0703-0.06940.44130.2626-0.50950.40620.0217-0.02380.4533-0.04730.2887-11.008616.3987-79.3815
467.02961.6849-1.16593.73470.15082.865-0.04640.0097-0.39010.07150.0622-0.26770.13510.2072-0.02560.1986-0.06-0.03660.10160.03520.1783-35.106311.693712.1192
472.82061.9620.84612.74720.87251.95980.0706-0.016-0.10160.04690.0856-0.06180.1293-0.0388-0.12930.1287-0.0361-0.00550.09870.02550.1711-29.558521.486114.0962
484.1492-1.17414.62924.4816-1.225.6848-0.0831-0.68510.06480.30.04140.0784-0.1415-0.45790.06630.222-0.06880.02170.12590.05150.2383-34.106820.294621.8695
495.21181.58830.86931.9599-0.08622.3415-0.13760.12680.0601-0.09770.0870.2269-0.1406-0.01440.05680.1688-0.0356-0.00490.07210.03310.1594-39.19819.714911.0988
504.9312.28172.27461.39330.81491.25370.0076-0.66390.0571-0.022-0.11580.07830.0467-0.0905-0.01910.1839-0.0312-0.00880.06790.00240.154-41.315313.83625.9686
511.7283-0.0404-1.52842.2358-0.50944.34560.09920.4205-0.242-0.443-0.08040.0911-0.0625-0.0774-0.09590.3711-0.0777-0.02840.0429-0.01940.2199-56.35987.069-17.9465
521.9414-0.569-0.97424.47611.00557.1444-0.1402-0.1432-0.2209-0.0484-0.0214-0.41040.93520.93580.15760.32010.0446-0.01880.16980.06390.3379-49.67360.6463-3.6275
533.9124-0.3927-1.64954.03872.33536.59380.0251-0.41640.1949-0.1743-0.03720.0496-0.2034-0.04270.0120.1985-0.03990.01730.06490.0360.1703-53.5911.5014-4.3427
541.80590.5178-0.70570.4212-0.94442.276-0.17680.4579-1.0322-0.67690.158-0.24180.80180.06560.00660.6513-0.06280.07020.148-0.09160.4592-53.9127-3.6963-17.3377
557.5388-2.29772.63987.1516-0.94316.43360.1241-0.3339-0.6101-0.4258-0.02550.25780.8654-0.2496-0.07490.3507-0.0486-0.0180.11950.07330.3304-59.0612-2.935-4.6841
561.81210.6940.56662.60061.22792.1689-0.1150.4320.1361-0.17450.00190.0524-0.22470.2820.07940.1763-0.0646-0.01650.23460.05120.1366-21.170628.0713-5.2125
573.53030.228-3.51968.37310.16483.6006-0.0944-0.35920.38790.5926-0.19350.1059-0.18710.27960.24240.1621-0.0315-0.02440.09960.05520.2045-25.073533.00047.8089
587.11912.57034.24452.8133-0.14564.27650.29560.0371-0.51860.0854-0.1705-0.19970.31210.5627-0.09080.17130.0050.01060.2168-0.00640.1547-29.087614.9524-19.7594
592.0650.7237-0.81381.1492-0.75952.2260.0943-0.19690-0.0038-0.06930.0278-0.09280.2310.0460.2295-0.0355-0.01380.06190.00080.1769-49.278814.3159-13.0724
602.80220.2138-1.40760.4145-0.46041.80730.19720.07690.21170.0665-0.01980.0878-0.24430.1052-0.15140.2609-0.0381-0.01670.07560.01080.1674-49.003220.2682-17.7361
617.495-1.5893-4.44130.47250.5654.35670.18240.3311-0.21360.052-0.13490.0847-0.0219-0.1205-0.02330.2113-0.0503-0.03430.12690.0590.1575-45.194819.034-25.4554
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )A0 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )A85 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 182 )A159 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 269 )A183 - 269
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )B1 - 11
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )B12 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )B20 - 30
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )B31 - 41
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 46 )B42 - 46
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 51 )B47 - 51
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 61 )B52 - 61
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 71 )B62 - 71
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 77 )B72 - 77
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 90 )B78 - 90
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 96 )B91 - 96
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 84 )C1 - 84
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 171 )C85 - 171
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 216 )C172 - 216
19X-RAY DIFFRACTION19chain 'C' and (resid 217 through 269 )C217 - 269
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 11 )D1 - 11
21X-RAY DIFFRACTION21chain 'D' and (resid 12 through 19 )D12 - 19
22X-RAY DIFFRACTION22chain 'D' and (resid 20 through 41 )D20 - 41
23X-RAY DIFFRACTION23chain 'D' and (resid 42 through 46 )D42 - 46
24X-RAY DIFFRACTION24chain 'D' and (resid 47 through 51 )D47 - 51
25X-RAY DIFFRACTION25chain 'D' and (resid 52 through 61 )D52 - 61
26X-RAY DIFFRACTION26chain 'D' and (resid 62 through 71 )D62 - 71
27X-RAY DIFFRACTION27chain 'D' and (resid 72 through 77 )D72 - 77
28X-RAY DIFFRACTION28chain 'D' and (resid 78 through 90 )D78 - 90
29X-RAY DIFFRACTION29chain 'D' and (resid 91 through 99 )D91 - 99
30X-RAY DIFFRACTION30chain 'E' and (resid 1 through 17 )E1 - 17
31X-RAY DIFFRACTION31chain 'E' and (resid 18 through 37 )E18 - 37
32X-RAY DIFFRACTION32chain 'E' and (resid 38 through 52 )E38 - 52
33X-RAY DIFFRACTION33chain 'E' and (resid 53 through 65 )E53 - 65
34X-RAY DIFFRACTION34chain 'E' and (resid 66 through 75 )E66 - 75
35X-RAY DIFFRACTION35chain 'E' and (resid 76 through 91 )E76 - 91
36X-RAY DIFFRACTION36chain 'E' and (resid 92 through 102 )E92 - 102
37X-RAY DIFFRACTION37chain 'E' and (resid 103 through 116 )E103 - 116
38X-RAY DIFFRACTION38chain 'E' and (resid 117 through 140 )E117 - 140
39X-RAY DIFFRACTION39chain 'E' and (resid 141 through 156 )E141 - 156
40X-RAY DIFFRACTION40chain 'E' and (resid 157 through 187 )E157 - 187
41X-RAY DIFFRACTION41chain 'E' and (resid 188 through 198 )E188 - 198
42X-RAY DIFFRACTION42chain 'F' and (resid 3 through 73 )F3 - 73
43X-RAY DIFFRACTION43chain 'F' and (resid 74 through 109 )F74 - 109
44X-RAY DIFFRACTION44chain 'F' and (resid 110 through 124 )F110 - 124
45X-RAY DIFFRACTION45chain 'F' and (resid 125 through 242 )F125 - 242
46X-RAY DIFFRACTION46chain 'G' and (resid 1 through 17 )G1 - 17
47X-RAY DIFFRACTION47chain 'G' and (resid 18 through 52 )G18 - 52
48X-RAY DIFFRACTION48chain 'G' and (resid 53 through 75 )G53 - 75
49X-RAY DIFFRACTION49chain 'G' and (resid 76 through 91 )G76 - 91
50X-RAY DIFFRACTION50chain 'G' and (resid 92 through 120 )G92 - 120
51X-RAY DIFFRACTION51chain 'G' and (resid 121 through 135 )G121 - 135
52X-RAY DIFFRACTION52chain 'G' and (resid 136 through 150 )G136 - 150
53X-RAY DIFFRACTION53chain 'G' and (resid 151 through 175 )G151 - 175
54X-RAY DIFFRACTION54chain 'G' and (resid 176 through 185 )G176 - 185
55X-RAY DIFFRACTION55chain 'G' and (resid 186 through 200 )G186 - 200
56X-RAY DIFFRACTION56chain 'H' and (resid 1 through 94 )H1 - 94
57X-RAY DIFFRACTION57chain 'H' and (resid 95 through 109 )H95 - 109
58X-RAY DIFFRACTION58chain 'H' and (resid 110 through 124 )H110 - 124
59X-RAY DIFFRACTION59chain 'H' and (resid 125 through 188 )H125 - 188
60X-RAY DIFFRACTION60chain 'H' and (resid 189 through 225 )H189 - 225
61X-RAY DIFFRACTION61chain 'H' and (resid 226 through 243 )H226 - 243

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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