[日本語] English
万見
- PDB-5d7j: Structure of human MR1-5-OP-RU in complex with human MAIT M33.64(... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 5d7j
タイトルStructure of human MR1-5-OP-RU in complex with human MAIT M33.64(Y95alphaF) 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 / Receptor / Antigen
機能・相同性
機能・相同性情報


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / negative regulation of receptor binding / positive regulation of receptor binding ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / iron ion transport / 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 / external side of plasma membrane / Golgi 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
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.97 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: Derived calculations / Refinement description
改定 2.02023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag
改定 2.12024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

-
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

-
集合体

登録構造単位
A: M33.64 TCR Alpha Chain
B: M33.64 TCR Beta Chain
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: Major histocompatibility complex class I-related gene protein
F: 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)188,08214
ポリマ－187,0818
非ポリマー1,0016
水22,6991260
1
A: M33.64 TCR Alpha Chain
B: M33.64 TCR Beta Chain
E: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,9496
ポリマ－93,5414
非ポリマー4082
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,1338
ポリマ－93,5414
非ポリマー5934
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)214.600, 69.590, 141.470
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number5
Space group name H-MC121

-
要素

-
タンパク質 , 4種, 8分子 AGBHCEDF

#1: タンパク質 M33.64 TCR Alpha Chain


分子量: 22767.283 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)
#2: 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)
#3: 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 / 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: 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

-
非ポリマー , 3種, 1266分子

#5: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物 ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


分子量: 316.310 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C12H20N4O6
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1260 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.74 Å3/Da / 溶媒含有率: 55.14 %
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

-
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: 1.97→35.76 Å / Num. obs: 135443 / % possible obs: 93.8 % / 冗長度: 3.6 % / Net I/σ(I): 8.4
反射 シェル解像度: 1.97→2 Å / 冗長度: 3.1 % / Mean I/σ(I) obs: 2 / % possible all: 77

-
位相決定

位相決定手法: 分子置換

-
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
PHENIX(phenix.refine: 1.9_1692)精密化
PDB_EXTRACT3.15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: 1.97→35.757 Å / SU ML: 0.21 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2224 6825 5.04 %
Rwork0.1791 128469 -
obs0.1813 135294 93.73 %
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: 115.22 Å2 / Biso mean: 32.7462 Å2 / Biso min: 5.57 Å2
精密化ステップサイクル: final / 解像度: 1.97→35.757 Å
タンパク質核酸リガンド溶媒全体
原子数12646 0 68 1260 13974
Biso mean--18.35 34.47 -
残基数----1602
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00813159
X-RAY DIFFRACTIONf_angle_d1.08717893
X-RAY DIFFRACTIONf_chiral_restr0.051913
X-RAY DIFFRACTIONf_plane_restr0.0052342
X-RAY DIFFRACTIONf_dihedral_angle_d14.2054692
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 (%)
1.966-1.98830.27231720.24893487365976
1.9883-2.01170.26251780.23373606378480
2.0117-2.03630.28212070.22473639384681
2.0363-2.0620.28052100.21813714392482
2.062-2.08920.25562150.21953781399683
2.0892-2.11780.29461960.21653784398084
2.1178-2.1480.24841880.21613961414987
2.148-2.18010.26492220.21153937415987
2.1801-2.21420.26512240.21184073429790
2.2142-2.25040.27731930.20964160435391
2.2504-2.28920.26682330.20114192442594
2.2892-2.33090.24842390.21344303454295
2.3309-2.37570.28112410.21144374461596
2.3757-2.42420.25632200.2054408462897
2.4242-2.47690.26492350.20314494472998
2.4769-2.53450.25452260.19744526475299
2.5345-2.59780.23362190.198645224741100
2.5978-2.66810.22242240.19934587481199
2.6681-2.74650.2822680.205444904758100
2.7465-2.83520.2512680.204145324800100
2.8352-2.93640.24432540.192945214775100
2.9364-3.0540.24312710.18944551482299
3.054-3.19290.21992370.179545454782100
3.1929-3.36110.20382500.171945654815100
3.3611-3.57150.20552480.163445434791100
3.5715-3.84690.19552270.155246424869100
3.8469-4.23350.19462470.143745574804100
4.2335-4.84480.15382550.121346054860100
4.8448-6.09910.16572360.147146374873100
6.0991-35.76250.20712220.17694733495598
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)
12.9079-0.2809-0.00741.3557-0.04361.7876-0.0140.28190.20010.0279-0.018-0.0806-0.09610.2569-0.00380.1134-0.03260.0140.21020.02310.1838-36.430737.048417.7293
20.96530.1795-0.39210.59730.33220.9067-0.0145-0.02580.10130.05-0.0073-0.0661-0.00870.07040.00880.0869-0.0031-0.00040.0930.01260.1296-46.657635.086120.7758
31.45380.067-0.65750.84290.1451.8943-0.0079-0.1399-0.17040.02020.0292-0.15620.22420.323-0.05350.12430.0132-0.0020.12330.01280.1586-42.131228.851521.3224
44.7546-0.5015-1.0480.6580.29480.9273-0.046-0.15610.0103-0.00450.0547-0.1320.09240.2772-0.01150.1276-0.00540.00370.18780.02760.1593-36.151332.856114.2296
52.10850.63151.01412.29191.63111.3694-0.07510.18290.1107-0.6291-0.0344-0.2935-0.15910.43980.0610.41540.07370.13930.45780.02920.4544-13.852229.4588-9.0088
61.1405-0.25150.12541.3164-0.06782.52070.0551-0.30330.5019-0.13710.13080.0705-0.65120.0446-0.00680.38930.03240.11840.4633-0.02680.6227-18.832438.41932.8807
71.6953-0.18890.1014.5763-1.99683.1218-0.0485-0.24350.2027-0.01260.117-0.03060.30480.3938-0.0180.23430.06930.07340.24010.05430.313-21.969826.17442.6782
81.4576-0.38490.35350.79420.44861.0064-0.119-0.10060.2620.03890.235-0.1980.03240.4127-0.05230.27360.05810.07250.29860.02960.365-19.225529.5180.0876
91.0725-0.40211.14510.156-0.44411.23720.0280.48750.4814-0.49120.1516-0.003-0.38190.02180.03290.5841-0.11840.23670.47870.05140.7514-12.395640.6378-10.1488
102.0778-0.59520.35731.96580.14481.69850.0517-0.20070.2660.14160.1335-0.1261-0.2320.3378-0.06460.3064-0.07460.07220.6387-0.1030.6743-9.452437.22012.6591
110.9536-0.0489-0.34840.5652-0.37680.8854-0.05610.2226-0.1124-0.3097-0.0427-0.08150.3586-0.21580.08270.2458-0.04270.03720.1534-0.0180.1486-55.88329.0232-2.3617
120.9803-0.0249-0.40280.5192-0.31131.7270.01670.07930.0184-0.0842-0.0551-0.03450.0321-0.10550.03770.1442-0.00270.00120.0925-0.01770.1288-57.883833.15643.5439
132.2277-0.6341-1.01350.46390.3081.00340.130.38360.5076-0.2734-0.0166-0.1703-0.331-0.01730.04760.362-0.00490.09080.130.05370.2928-43.493437.3886-14.6104
141.2424-0.07820.37981.0799-0.07091.7977-0.0211-0.0147-0.0612-0.02380.0585-0.14690.34970.2768-0.01830.33120.0740.12250.18830.00070.3023-24.782224.771-7.6911
151.3733-0.36620.52522.1011-0.41862.43280.14020.17730.063-0.42950.03830.09470.2250.0058-0.13360.3845-0.03260.12720.1464-0.02180.2493-36.097426.678-19.5825
161.66190.73140.25021.82470.16451.5862-0.09250.1899-0.37170.09590.0629-0.20670.22290.16170.00650.1735-0.03370.00370.21540.02460.1657-47.673520.520279.8794
175.32031.51651.39260.8860.21281.37870.1542-0.044-0.22260.12430.0049-0.04670.06420.0255-0.12130.2606-0.042-0.07110.20240.03760.2453-51.742723.570685.572
180.92750.67530.33981.04360.67771.44030.05350.31160.1385-0.0675-0.01740.11250.22620.1025-0.06350.148-0.0528-0.03560.2850.07970.1673-45.675532.122679.2365
191.30840.38410.50350.78810.0031.1686-0.00520.01130.1260.0771-0.0210.11580.0255-0.04290.01760.1639-0.0475-0.01810.18380.04880.1919-49.459631.81289.0315
202.98250.7740.42180.78750.26090.8839-0.1106-0.16810.0615-0.06040.01760.1904-0.0858-0.07210.03450.164-0.0554-0.0420.24060.07030.1961-55.637429.334579.7717
212.07080.73980.71810.81710.53130.68640.06590.334-0.12470.04780.1055-0.10620.04830.0733-0.10710.1852-0.0752-0.04080.31320.02110.1902-44.243627.978378.4322
222.55230.69591.25821.4024-0.84991.7857-0.083-0.1640.2151-0.0903-0.01560.24520.08-0.60260.01790.2964-0.1188-0.00830.40390.04570.2694-77.375816.48369.0198
231.0913-0.0660.09010.7379-0.65292.52280.0854-0.1031-0.3322-0.57720.12530.01180.73410.3563-0.11140.5667-0.0703-0.00820.2670.00240.222-69.061313.254358.3779
241.00190.61860.01491.20370.80262.70190.1558-0.30580.2339-0.2388-0.0129-0.17680.0738-0.05830.00420.3258-0.03660.0390.36830.04350.1873-69.605422.127265.1142
251.61870.3209-0.22360.221-0.46721.6936-0.02750.0388-0.3002-0.4668-0.0567-0.01660.5995-0.39940.05660.5348-0.07860.05980.24090.03010.2359-70.149912.71257.461
263.3501-0.33240.79531.4288-0.49161.6624-0.0776-0.1224-0.5136-0.4035-0.0372-0.01750.657-0.12430.03320.7074-0.17710.05730.37110.11110.4187-74.37336.508165.2427
270.1938-0.03360.10450.63230.37230.7549-0.07290.52680.0879-0.4429-0.03290.295-0.42130.2261-0.0240.3983-0.1452-0.11820.68230.13420.1707-40.925239.791361.8771
281.00150.29940.08760.38590.28570.9796-0.09280.45550.0088-0.13250.1205-0.0361-0.10380.4671-0.01420.2878-0.1325-0.05430.65740.09830.197-35.10436.287264.9361
291.31460.22361.28910.85571.04083.0369-0.03160.23540.2397-0.23830.00890.2347-0.3287-0.10670.08780.231-0.0652-0.07160.39260.13870.2297-43.291642.010475.6318
302.28510.98941.60940.93030.39911.31270.169-0.2498-0.33820.05750.005-0.29760.43120.5705-0.05620.31470.0078-0.01590.52470.04980.2318-45.302724.851848.731
311.7082-0.3556-0.37711.4028-0.47611.49180.3101-0.23130.0226-0.2239-0.09810.0107-0.34450.0216-0.16540.33-0.10830.02020.36680.02140.1561-69.535624.127154.6907
321.66550.1129-0.40181.37710.31632.07020.2365-0.39540.14170.1703-0.3336-0.4356-0.09320.64830.09260.4407-0.03750.08510.4120.11570.2107-59.62123.137856.92
331.28340.2378-0.93010.5143-0.28341.24190.3688-0.35220.32760.087-0.03880.0813-0.45730.2366-0.16450.3845-0.09120.00380.41230.08590.2069-65.323829.572451.2436
344.70350.1587-1.24930.4743-0.37281.05520.2687-0.4168-0.02560.0762-0.1487-0.0234-0.1926-0.0304-0.02870.2546-0.0984-0.00540.40860.12710.2338-60.902928.773643.2444
350.90370.184-0.13091.4437-0.45871.12650.03960.12510.0914-0.0368-0.01650.18210.0047-0.0164-0.0020.1060.0040.02020.0761-0.03260.1506-76.553233.790420.8974
361.31780.202-0.00791.179-0.62370.63190.067-0.098-0.15550.1832-0.0963-0.0610.0650.07480.02160.1416-0.02460.02070.0902-0.01480.1374-68.785226.538431.5191
371.56830.1951-0.07491.11530.0731.3058-0.0183-0.3046-0.18290.0565-0.06290.08520.1138-0.26160.03990.2511-0.01220.08210.2064-0.04030.2463-92.365844.738149.5621
380.91220.2518-0.31890.99490.39941.08410.1601-0.2713-0.19180.2506-0.03440.24710.27790.0003-0.01870.3524-0.0040.05840.18690.03420.2824-91.566438.76850.0651
391.1238-0.0015-0.01331.30330.02782.28990.0088-0.3198-0.1960.2383-0.13920.08330.3054-0.26390.10650.2366-0.04170.06170.27230.00170.2305-90.803244.04555.0726
401.1057-1.1690.59141.7424-0.91650.5028-0.05290.1068-0.02180.014-0.1515-0.06840.0278-0.08210.13250.1759-0.02970.03290.1382-0.06940.2543-95.60729.926335.1349
411.3591-0.3840.36680.4911-0.46640.4341-0.2191-0.13230.45930.1897-0.31220.3253-0.2462-0.4577-0.14890.39590.1401-0.00620.3258-0.19670.5695-104.06251.533639.3171
421.0722-1.3389-0.59133.11451.09780.5667-0.06310.0210.1893-0.056-0.08360.176-0.2729-0.18570.09880.19040.04170.00470.1485-0.05880.2722-97.04339.870533.1968
433.363-2.7305-1.39642.76810.69510.9759-0.06680.32730.0851-0.5278-0.16060.2066-0.2189-0.60330.17630.2499-0.0151-0.08520.2708-0.07320.292-98.459231.800525.7223
445.65840.277-1.51771.024-0.36251.77820.16120.41760.3837-0.52230.00990.236-0.2624-0.402-0.11150.35730.1584-0.14410.4617-0.07620.4815-104.464641.773723.4705
452.1136-1.66430.76332.5502-0.64570.8869-0.12230.120.0107-0.13220.08010.05220.0735-0.09010.05290.2008-0.01310.04770.1194-0.01180.1841-84.451231.396930.057
464.6574-3.4968-0.36652.77980.12780.5405-0.13840.28110.4472-0.2988-0.1224-0.0341-0.1973-0.44560.16160.27960.0891-0.06850.2059-0.08040.3004-96.608741.496529.7388
474.85070.0473-0.02255.05092.36282.8344-0.1015-0.0968-0.08220.2386-0.02870.47790.1628-0.44670.06940.40910.1791-0.02050.5044-0.08450.9426-114.241245.721535.1779
481.7415-1.8011-0.2382.1974-0.04810.58540.1125-0.14550.0439-0.2608-0.09780.2724-0.0524-0.13730.00390.16230.0116-0.06150.2867-0.14890.3504-103.278832.74628.607
492.7203-1.92640.71684.73330.41433.7803-0.013-0.0634-0.3001-0.2379-0.04790.58340.1723-0.4893-0.01690.2394-0.07410.00020.2671-0.12970.3452-102.227122.163627.6358
502.6968-0.8114-0.22963.28230.25422.2898-0.2242-0.36310.3310.294-0.16410.2468-0.1736-0.37820.1590.20810.01770.03090.3611-0.17550.3949-106.974436.979237.474
511.11770.23390.27191.20860.14981.5043-0.02670.47620.1589-0.22120.1129-0.06750.04730.1806-0.04620.1418-0.0609-0.02140.45980.07120.1919-21.573747.940584.728
521.19110.50590.23031.64420.20560.96110.10260.14590.18660.0615-0.04420.20220.0147-0.002-0.05910.127-0.0272-0.02890.27260.06070.2178-31.671348.409195.0768
530.8603-0.5596-0.24110.4392-0.1060.79890.02180.1579-0.03560.10880.1762-0.3142-0.01540.2327-0.09410.23010.0627-0.14010.3245-0.03540.378-2.136242.0538107.6168
540.98810.55790.78112.15152.61524.1633-0.1308-0.19510.4630.00090.0333-0.0188-0.2886-0.22470.0190.27210.1019-0.14440.2903-0.06910.365-4.046248.4781113.8477
550.8360.16290.15551.51750.65262.2035-0.06480.13340.20260.1407-0.09490.1367-0.4392-0.16840.09110.25430.0724-0.08380.3302-0.02280.358-5.141752.5479112.8732
560.60130.26940.03492.21931.34371.9861-0.1444-0.40770.2410.184-0.01080.0248-0.4292-0.37440.06340.35370.0875-0.15480.3877-0.1010.3596-2.946748.2534123.1504
573.546-0.9275-1.3730.3480.40020.56770.09190.26630.42710.0843-0.054-0.1431-0.17080.1722-0.01610.2828-0.0457-0.08930.40380.06820.5567-8.406662.031599.1748
581.0322-0.45451.09071.06560.25121.7615-0.12760.01410.03410.0507-0.0575-0.461-0.19230.4409-0.03210.1190.0431-0.23360.59030.03910.941910.685449.8022101.716
590.5671-0.1012-0.00450.6640.00010.55020.09020.70220.4231-0.2152-0.0474-0.479-0.33730.5088-0.0859-0.1489-0.2327-0.06390.68320.28310.7518-0.944559.066791.7097
606.298-1.8948-1.34392.04711.03711.5047-0.01570.07860.0238-0.04680.1273-0.1530.0660.18310.00630.1534-0.0069-0.0280.41910.0520.2661-16.70354.184894.0945
612.82930.520.16090.42370.09980.8319-0.06170.2441-0.0599-0.1149-0.0726-0.53720.14810.5686-0.1041-0.3844-0.03850.04980.75830.15460.4789-0.652353.993792.9064
620.10080.1221-0.07190.27380.0410.18110.1334-0.07240.02520.06940.0421-0.18860.03070.21430.07660.263-0.0249-0.24931.0593-0.00851.142816.026860.275198.4433
633.2324-0.98630.10741.0037-0.05710.56190.1464-0.04420.2804-0.09970.1234-0.4627-0.26350.21320.05780.3134-0.29030.00540.59020.48721.0995-3.825768.310592.9743
642.4659-0.6441-0.0673.8935-0.27613.2376-0.04-0.06110.12910.13310.2654-0.2281-0.08460.26430.02150.4018-0.1134-0.27920.51510.15820.92954.655763.4504100.8023
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 1 through 17 )G0
2X-RAY DIFFRACTION2chain 'G' and (resid 18 through 37 )G0
3X-RAY DIFFRACTION3chain 'G' and (resid 38 through 91 )G0
4X-RAY DIFFRACTION4chain 'G' and (resid 92 through 116 )G0
5X-RAY DIFFRACTION5chain 'G' and (resid 117 through 135 )G0
6X-RAY DIFFRACTION6chain 'G' and (resid 136 through 150 )G0
7X-RAY DIFFRACTION7chain 'G' and (resid 151 through 165 )G0
8X-RAY DIFFRACTION8chain 'G' and (resid 166 through 175 )G0
9X-RAY DIFFRACTION9chain 'G' and (resid 176 through 185 )G0
10X-RAY DIFFRACTION10chain 'G' and (resid 186 through 198 )G0
11X-RAY DIFFRACTION11chain 'H' and (resid 3 through 37 )H0
12X-RAY DIFFRACTION12chain 'H' and (resid 38 through 108 )H0
13X-RAY DIFFRACTION13chain 'H' and (resid 109 through 123 )H0
14X-RAY DIFFRACTION14chain 'H' and (resid 124 through 214 )H0
15X-RAY DIFFRACTION15chain 'H' and (resid 215 through 243 )H0
16X-RAY DIFFRACTION16chain 'A' and (resid 1 through 13 )A0
17X-RAY DIFFRACTION17chain 'A' and (resid 14 through 25 )A0
18X-RAY DIFFRACTION18chain 'A' and (resid 26 through 42 )A0
19X-RAY DIFFRACTION19chain 'A' and (resid 43 through 75 )A0
20X-RAY DIFFRACTION20chain 'A' and (resid 76 through 91 )A0
21X-RAY DIFFRACTION21chain 'A' and (resid 92 through 108 )A0
22X-RAY DIFFRACTION22chain 'A' and (resid 109 through 120 )A0
23X-RAY DIFFRACTION23chain 'A' and (resid 121 through 150 )A0
24X-RAY DIFFRACTION24chain 'A' and (resid 151 through 165 )A0
25X-RAY DIFFRACTION25chain 'A' and (resid 166 through 185 )A0
26X-RAY DIFFRACTION26chain 'A' and (resid 186 through 198 )A0
27X-RAY DIFFRACTION27chain 'B' and (resid 3 through 37 )B0
28X-RAY DIFFRACTION28chain 'B' and (resid 38 through 94 )B0
29X-RAY DIFFRACTION29chain 'B' and (resid 95 through 108 )B0
30X-RAY DIFFRACTION30chain 'B' and (resid 109 through 123 )B0
31X-RAY DIFFRACTION31chain 'B' and (resid 124 through 161 )B0
32X-RAY DIFFRACTION32chain 'B' and (resid 162 through 187 )B0
33X-RAY DIFFRACTION33chain 'B' and (resid 188 through 224 )B0
34X-RAY DIFFRACTION34chain 'B' and (resid 225 through 242 )B0
35X-RAY DIFFRACTION35chain 'C' and (resid 1 through 83 )C0
36X-RAY DIFFRACTION36chain 'C' and (resid 84 through 171 )C0
37X-RAY DIFFRACTION37chain 'C' and (resid 172 through 216 )C0
38X-RAY DIFFRACTION38chain 'C' and (resid 217 through 237 )C0
39X-RAY DIFFRACTION39chain 'C' and (resid 238 through 269 )C0
40X-RAY DIFFRACTION40chain 'D' and (resid 1 through 11 )D0
41X-RAY DIFFRACTION41chain 'D' and (resid 12 through 19 )D0
42X-RAY DIFFRACTION42chain 'D' and (resid 20 through 30 )D0
43X-RAY DIFFRACTION43chain 'D' and (resid 31 through 41 )D0
44X-RAY DIFFRACTION44chain 'D' and (resid 42 through 51 )D0
45X-RAY DIFFRACTION45chain 'D' and (resid 52 through 61 )D0
46X-RAY DIFFRACTION46chain 'D' and (resid 62 through 71 )D0
47X-RAY DIFFRACTION47chain 'D' and (resid 72 through 77 )D0
48X-RAY DIFFRACTION48chain 'D' and (resid 78 through 84 )D0
49X-RAY DIFFRACTION49chain 'D' and (resid 85 through 90 )D0
50X-RAY DIFFRACTION50chain 'D' and (resid 91 through 98 )D0
51X-RAY DIFFRACTION51chain 'E' and (resid 1 through 84 )E0
52X-RAY DIFFRACTION52chain 'E' and (resid 85 through 171 )E0
53X-RAY DIFFRACTION53chain 'E' and (resid 172 through 195 )E0
54X-RAY DIFFRACTION54chain 'E' and (resid 196 through 216 )E0
55X-RAY DIFFRACTION55chain 'E' and (resid 217 through 245 )E0
56X-RAY DIFFRACTION56chain 'E' and (resid 246 through 269 )E0
57X-RAY DIFFRACTION57chain 'F' and (resid 1 through 11 )F0
58X-RAY DIFFRACTION58chain 'F' and (resid 12 through 19 )F0
59X-RAY DIFFRACTION59chain 'F' and (resid 20 through 51 )F0
60X-RAY DIFFRACTION60chain 'F' and (resid 52 through 61 )F0
61X-RAY DIFFRACTION61chain 'F' and (resid 62 through 71 )F0
62X-RAY DIFFRACTION62chain 'F' and (resid 72 through 77 )F0
63X-RAY DIFFRACTION63chain 'F' and (resid 78 through 90 )F0
64X-RAY DIFFRACTION64chain 'F' and (resid 91 through 97 )F0

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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