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- PDB-5d7i: Structure of human MR1-Ac-6-FP in complex with human MAIT M33.64 TCR -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 5d7i
タイトルStructure of human MR1-Ac-6-FP in complex with human MAIT M33.64 TCR
要素
  • Beta-2-microglobulin
  • M33.64 TCR Alpha Chain
  • M33.64 TCR Beta Chain
  • Major histocompatibility complex class I-related gene protein
キーワードIMMUNE SYSTEM / Antigen / 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 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
Chem-30W / PROLINE / 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. / Woolley, R.E. / Rossjohn, J.
引用ジャーナル: Immunity / 年: 2016
タイトル: Diversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition.
著者: Gherardin, N.A. / Keller, A.N. / Woolley, R.E. / Le Nours, J. / Ritchie, D.S. / Neeson, P.J. / Birkinshaw, R.W. / Eckle, S.B. / Waddington, J.N. / Liu, L. / Fairlie, D.P. / Uldrich, A.P. / ...著者: Gherardin, N.A. / Keller, A.N. / Woolley, R.E. / Le Nours, J. / Ritchie, D.S. / Neeson, P.J. / Birkinshaw, R.W. / Eckle, S.B. / Waddington, J.N. / Liu, L. / Fairlie, D.P. / Uldrich, A.P. / Pellicci, D.G. / McCluskey, J. / Godfrey, D.I. / Rossjohn, J.
履歴
登録2015年8月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年1月27日Provider: repository / タイプ: Initial release
改定 1.12016年2月3日Group: Database references
改定 1.22016年2月10日Group: Refinement description
改定 1.32023年9月27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 / diffrn_radiation_wavelength / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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
G: M33.64 TCR Alpha Chain
H: M33.64 TCR Beta Chain
E: M33.64 TCR Alpha Chain
F: M33.64 TCR Beta Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,73122
ポリマ－187,1138
非ポリマー1,61814
水23,2571291
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: M33.64 TCR Alpha Chain
H: M33.64 TCR Beta Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,55013
ポリマ－93,5574
非ポリマー9939
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-46 kcal/mol
Surface area36060 Å2
手法PISA
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: M33.64 TCR Alpha Chain
F: M33.64 TCR Beta Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,1819
ポリマ－93,5574
非ポリマー6255
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-45 kcal/mol
Surface area37020 Å2
手法PISA
単位格子
Length a, b, c (Å)214.300, 69.660, 141.190
Angle α, β, γ (deg.)90.000, 103.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11H-637-

HOH

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要素

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タンパク質 , 4種, 8分子 ACBDGEHF

#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: Extracellular domain residues 23-292 / 由来タイプ: 組換発現 / 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: 11879.356 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: 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
#3: タンパク質 M33.64 TCR Alpha Chain


分子量: 22783.283 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/TRAV / 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 M33.64 TCR Beta Chain


分子量: 27182.260 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 , 4種, 1305分子

#5: 化合物 ChemComp-PRO / PROLINE / プロリン


タイプ: L-peptide linking / 分子量: 115.130 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C5H9NO2
#6: 化合物 ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin / 2-(アセチルアミノ)-4-オキソ-3,4-ジヒドロプテリジン-6-カルボアルデヒド


分子量: 233.184 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C9H7N5O3
#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: 10 / 由来タイプ: 合成 / 式: C3H8O3
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1291 / 由来タイプ: 天然 / 式: H2O

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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: 2.74 Å3/Da / 溶媒含有率: 55.05 %
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: 0.954 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: 0.954 Å / 相対比: 1
反射解像度: 2→51.74 Å / Num. obs: 133791 / % possible obs: 98.1 % / 冗長度: 3.7 % / Net I/σ(I): 8.7
反射 シェル解像度: 2→2.07 Å / 冗長度: 3.6 % / Mean I/σ(I) obs: 1.2 / % possible all: 97

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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
PHENIX(phenix.refine: 1.9_1692)精密化
Aimlessデータスケーリング
PHASER位相決定
PDB_EXTRACT3.15データ抽出
iMOSFLMデータ削減
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→51.74 Å / SU ML: 0.23 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 23.54 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2201 6637 4.96 %
Rwork0.1777 127122 -
obs0.1798 133759 97.81 %
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
原子変位パラメータBiso max: 132.71 Å2 / Biso mean: 39.9361 Å2 / Biso min: 12.84 Å2
精密化ステップサイクル: final / 解像度: 2→51.74 Å
タンパク質核酸リガンド溶媒全体
原子数12761 0 106 1291 14158
Biso mean--45.36 42.82 -
残基数----1611
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00713296
X-RAY DIFFRACTIONf_angle_d1.08618068
X-RAY DIFFRACTIONf_chiral_restr0.0461920
X-RAY DIFFRACTIONf_plane_restr0.0042379
X-RAY DIFFRACTIONf_dihedral_angle_d13.7854761
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 (%)
2-2.02270.33882140.29734182439697
2.0227-2.04650.35812200.28254236445697
2.0465-2.07150.31942250.27524052427797
2.0715-2.09770.27291780.25134252443097
2.0977-2.12530.25351990.23234215441497
2.1253-2.15440.29732240.24044140436497
2.1544-2.18520.30181930.23024240443397
2.1852-2.21780.28352330.22494142437597
2.2178-2.25250.28732500.22844240449098
2.2525-2.28940.27832350.2184097433297
2.2894-2.32890.24272160.21124247446398
2.3289-2.37120.26782300.20774207443798
2.3712-2.41690.26032270.19914206443398
2.4169-2.46620.24832250.1994224444998
2.4662-2.51980.23972280.19814194442298
2.5198-2.57840.25612130.19114276448998
2.5784-2.64290.23792320.19154151438398
2.6429-2.71440.24082240.19274292451698
2.7144-2.79420.22562390.19384212445198
2.7942-2.88440.24432320.18694270450298
2.8844-2.98750.22782360.17954205444198
2.9875-3.10710.20922140.17564263447798
3.1071-3.24850.21362040.17454296450098
3.2485-3.41970.20822210.16654274449598
3.4197-3.63390.19092140.15294286450098
3.6339-3.91440.19412210.14924291451299
3.9144-4.30820.17372340.14024290452498
4.3082-4.93110.14552100.12094315452598
4.9311-6.2110.18062040.15384375457999
6.211-51.76040.21022420.17174452469499
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)
11.2526-0.0418-0.02642.8062-0.96561.58130.06460.00680.01590.0298-0.0550.18690.00730.00850.00780.1312-0.01240.02680.1273-0.03490.161177.06162.389297.4714
21.3168-0.3218-0.61860.91750.34431.10780.0387-0.206-0.0101-0.0144-0.0112-0.0027-0.02690.0363-0.02890.2007-0.0631-0.04190.2130.00420.1613177.614663.5087311.1486
32.71540.55250.02033.52480.28792.44170.0578-0.4131-0.13950.2141-0.1198-0.03670.1671-0.01620.06640.21610.00730.03650.2262-0.00820.2134163.089672.8006326.1739
422-0.1019222-2.6981-0.61164.68293.45160.377-1.2781-1.82981.10852.34440.24210.18230.47450.9783-0.18741.1237153.52978.9011338.938
51.7524-1.53560.61562.2121-1.57431.47980.04370.107-0.16450.0552-0.35340.0093-0.0111-0.24480.24810.188-0.0157-0.01840.2737-0.03790.325157.591560.3835308.9888
62.6376-0.35671.64561.3948-1.00071.4714-0.2153-0.31421.34330.4672-0.20030.3848-1.1457-0.85940.27470.51240.1379-0.06280.4359-0.17810.6982148.962181.8096313.3178
73.1127-1.6416-1.0256.30781.98592.69360.00750.08910.3055-0.5224-0.10430.432-0.4063-0.2540.09350.2437-0.0035-0.02870.2221-0.0270.3148156.026170.3452307.0697
88.8966-6.1782-1.6427.7291.63852.60530.23060.6068-0.5117-0.667-0.46270.4793-0.2219-0.59690.21070.2297-0.0504-0.03660.3409-0.07330.2559154.666662.2641299.5921
95.72340.8886-4.28886.71421.01313.6547-0.22780.76330.3682-1.1229-0.25270.81860.2893-1.33870.40060.5230.0847-0.20180.6405-0.05390.5164143.026269.9526298.3283
102.0687-1.93482.06177.1691-1.43433.92950.07091.35040.6905-1.260.18970.4692-0.9142-0.4373-0.1030.77570.0686-0.05660.69050.08440.5081153.748374.3055296.1311
113.2514-2.82691.97393.1302-1.66381.27080.0310.04940.1717-0.3822-0.0614-0.20290.2339-0.1517-0.00730.2859-0.03260.05460.2373-0.06360.2389168.740462.0037303.8762
128.284-4.31820.08294.96480.41642.9853-0.01550.68750.7021-0.3871-0.28820.0684-0.4076-0.4290.29820.30330.0207-0.04940.2928-0.00420.2834156.451671.9925303.6044
137.30450.3271-1.92874.9941-1.19467.27980.17620.1706-0.13020.4509-0.0910.48530.2262-1.0481-0.12540.39440.1087-0.01750.5197-0.10670.9959139.037775.5335309.2533
142.9424-2.4744-0.37395.9667-0.70981.74950.12920.303-0.2351-0.6705-0.36780.82990.1128-0.64330.27150.2643-0.0207-0.06510.4267-0.150.3612150.347458.6947302.0728
156.83680.97591.07852.49143.1026.7581-0.19-0.01520.71570.4542-0.60231.0455-0.0047-0.64140.64390.2626-0.0460.03570.4375-0.10440.4111146.282867.7252311.7725
161.54540.20130.09072.2963-0.45361.46690.07-0.3880.1760.2559-0.0230.14650.0406-0.1021-0.04920.2230.0402-0.0070.4943-0.0490.2735133.82443.8597327.063
171.6580.07550.07862.3761-0.4250.71760.0827-0.02120.1495-0.145-0.0315-0.17890.08150.0343-0.04690.19720.036-0.01950.3531-0.03840.2243143.77243.9851316.2365
182.1277-0.27711.25932.4951-1.44325.1168-0.09990.15160.441-0.1641-0.12340.0744-0.51610.21840.21330.27-0.0559-0.11340.33430.04180.4084115.472545.184296.2173
192.000122.00021.99991.99991.9999-1.1444-1.2585-5.1437-0.50691.3883-19.6242.7490.749-0.28580.82450.1584-0.26441.05570.01941.3237105.615745.9209282.819
203.35590.7324-1.79550.3582-0.59591.1279-0.0696-0.45430.6299-0.0157-0.01990.3404-0.2609-0.00280.09370.26710.0435-0.09610.3613-0.01920.6727120.65957.8391312.1238
213.494-2.3551.10011.8273-1.03210.7136-0.60030.5141-0.2822-0.4979-0.16820.6552-0.2566-1.06480.18090.37620.0122-0.30610.7312-0.17480.9483101.072345.8784309.3696
220.441-0.73540.15351.2094-0.12681.88920.1684-0.40190.14590.0601-0.0670.42130.1425-0.1527-0.10510.19650.0459-0.04210.4616-0.12330.554113.384651.2384314.7365
234.0509-0.2619-0.35030.1961-0.46191.578-0.3793-1.12720.92250.2344-0.08171.1074-0.7281-0.39640.2130.31210.13640.01020.5746-0.30711.0439117.381559.0326321.4141
240.64070.54150.81411.41010.81691.6120.0756-0.31330.54230.28210.32910.0045-0.4181-0.3195-0.12460.00530.3981-0.27091.1446-0.64061.6232103.444460.5529322.1729
252.5423.0703-2.17253.87-3.19563.85520.4329-1.35190.66211.48870.46220.735-0.6432-0.4141-0.85410.5706-0.01580.16341.087-0.18640.7271109.851451.0634325.5725
262.92522.1543-3.12622.7926-1.89873.53350.0995-0.17630.03430.0283-0.06450.52080.1854-0.4090.03490.2656-0.0255-0.01440.5105-0.07880.3851128.634649.7894317.2107
275.4234-1.3784-0.65790.7415-0.351.64680.0437-0.89050.15160.1045-0.02410.65740.2003-0.5726-0.08690.23840.00010.01260.5913-0.12060.5868112.736149.9562318.4033
281.66610.3035-1.74788.4862.89353.07220.1491-0.1190.4148-0.5890.27130.0089-0.533-0.4391-0.31260.51340.1612-0.17041.0873-0.23941.379396.541956.9456312.138
293.79370.4273-1.71272.2719-1.1811.24520.2358-0.22330.30280.1173-0.0610.85070.09090.1014-0.19870.38540.1002-0.00550.562-0.26520.9525110.761960.7141317.9557
301.46481.1365-0.97850.9491-0.36462.866-0.21650.04280.66630.07250.30090.9089-0.7931-0.8589-0.10380.43570.2084-0.11970.5643-0.34361.3852121.091767.5492318.458
313.59621.429-1.90748.6499-1.04711.024-0.30730.57330.7213-0.93870.07010.37980.02420.10080.12850.63390.1812-0.36630.5544-0.08280.8738107.913459.5947309.2803
322.89020.2728-0.58890.88080.36191.75960.0131-0.0586-0.12020.0743-0.0111-0.09630.09970.31190.01430.16010.005-0.01240.16120.03120.1739212.367862.5231293.2637
334.46550.00840.40363.7173-0.13245.06960.00320.04070.5423-0.26710.0593-0.4065-0.15250.7349-0.06680.24180.01750.06650.34940.00690.4636237.133563.5466272.3131
341.78620.0461-0.80351.0392-0.43753.1036-0.01320.1572-0.0316-0.1472-0.0563-0.01180.1566-0.20930.06870.1936-0.0045-0.00670.1271-0.01820.1869196.072962.2711275.6006
355.8258-1.2785-3.23981.42521.7282.76080.21550.38710.4913-0.1955-0.0513-0.258-0.5856-0.0434-0.14990.4257-0.0220.05390.22120.03320.3217209.983467.8556259.5251
361.630.12350.93141.848-0.62283.28410.0182-0.0094-0.14670.02830.0575-0.20420.42490.3531-0.08230.33410.06540.08340.2023-0.01370.3139228.682855.4346266.4636
374.0024-1.31691.16454.567-0.64923.8216-0.09710.4748-0.2045-0.58760.10470.28230.273-0.0382-0.08580.3658-0.0610.04630.2103-0.03960.2654216.815257.3251254.3896
382.8332-1.80430.68512.1428-0.86961.4215-0.0001-0.08740.1308-0.0751-0.0168-0.05580.0354-0.05080.01820.22920.032-0.02670.2634-0.05830.214161.985124.5182327.3161
392.381-1.11020.62871.382-0.32030.75750.04590.234-0.11120.2135-0.0378-0.10520.07280.14710.00590.29610.001-0.01460.2277-0.02510.1875175.784116.3452344.4406
405.67282.0905-0.89418.5487-4.20772.54060.04910.51630.1072-0.4024-0.33260.56540.6186-0.74670.34360.4667-0.0017-0.02060.5389-0.17440.3995178.13726.2443342.2957
413.8203-0.0047-1.16562.08651.22623.5238-0.04420.1509-0.43020.3798-0.0436-0.01190.6187-0.07690.07910.4420.0131-0.00440.2931-0.05640.2633183.17119.0414349.8634
421.5209-0.51140.50771.6398-1.28742.2658-0.0571-0.46990.08090.36990.0561-0.04-0.2526-0.2931-0.0060.34540.0817-0.06390.623-0.10720.2434150.348633.9343345.984
434.5348-1.21352.66012.2158-1.48223.86570.1730.3385-0.3186-0.36730.15550.31150.5274-0.7838-0.29910.3713-0.0307-0.04420.5299-0.0310.2843157.564520.5205362.1017
444.2780.5548-1.54262.13940.92233.54160.1920.4779-0.01960.1533-0.12040.1303-0.1422-0.4021-0.06590.34550.0622-0.02010.2989-0.00940.1753179.03219.7775355.1795
455.94910.1994-3.71430.6555-0.15443.13050.40920.38340.1674-0.0526-0.1690.0024-0.4313-0.3112-0.20250.4040.0645-0.02050.3492-0.09890.2779173.679326.1144365.6655
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 114 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 203 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 269 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 301 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 46 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 51 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 61 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 71 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 77 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 90 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 84 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 171 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 269 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 301 through 301 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 11 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 12 through 19 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 20 through 30 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 31 through 41 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 42 through 46 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 47 through 51 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 52 through 61 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 62 through 71 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 72 through 77 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 78 through 83 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 84 through 90 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 91 through 98 )D0
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 116 )G0
33X-RAY DIFFRACTION33chain 'G' and (resid 117 through 198 )G0
34X-RAY DIFFRACTION34chain 'H' and (resid 3 through 108 )H0
35X-RAY DIFFRACTION35chain 'H' and (resid 109 through 123 )H0
36X-RAY DIFFRACTION36chain 'H' and (resid 124 through 214 )H0
37X-RAY DIFFRACTION37chain 'H' and (resid 215 through 243 )H0
38X-RAY DIFFRACTION38chain 'E' and (resid 1 through 91 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 92 through 137 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 138 through 147 )E0
41X-RAY DIFFRACTION41chain 'E' and (resid 148 through 200 )E0
42X-RAY DIFFRACTION42chain 'F' and (resid 1 through 108 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 109 through 123 )F0
44X-RAY DIFFRACTION44chain 'F' and (resid 124 through 201 )F0
45X-RAY DIFFRACTION45chain 'F' and (resid 202 through 243 )F0

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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