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- PDB-5d7l: Structure of human MR1-5-OP-RU in complex with human MAV36 TCR -

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基本情報

登録情報
データベース: PDB / ID: 5d7l
タイトルStructure of human MR1-5-OP-RU in complex with human MAV36 TCR
要素
  • Beta-2-microglobulin
  • MAV36 TCR Alpha Chain
  • MAV36 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 / : / : / 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
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 Å
データ登録者Keller, A.N. / 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 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 / citation / database_2 / diffrn_radiation_wavelength / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.journal_id_CSD / _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 / _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 2.12024年10月23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: MAV36 TCR Alpha Chain
E: MAV36 TCR Beta Chain
F: Beta-2-microglobulin
G: MAV36 TCR Alpha Chain
H: MAV36 TCR Beta Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,77210
ポリマ－188,1398
非ポリマー6332
水00
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,9073
ポリマ－43,5912
非ポリマー3161
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-14 kcal/mol
Surface area19380 Å2
手法PISA
2
C: 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)43,9073
ポリマ－43,5912
非ポリマー3161
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-16 kcal/mol
Surface area18860 Å2
手法PISA
3
D: MAV36 TCR Alpha Chain
E: MAV36 TCR Beta Chain


分子量 (理論値)分子数
合計 (水以外)50,4782
ポリマ－50,4782
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-28 kcal/mol
Surface area21550 Å2
手法PISA
4
G: MAV36 TCR Alpha Chain
H: MAV36 TCR Beta Chain


分子量 (理論値)分子数
合計 (水以外)50,4782
ポリマ－50,4782
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-28 kcal/mol
Surface area21570 Å2
手法PISA
単位格子
Length a, b, c (Å)89.280, 222.432, 98.979
Angle α, β, γ (deg.)90.000, 100.150, 90.000
Int Tables number5
Space group name H-MI121
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 F
13chain D
23chain G
14chain E
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
11ARGARGVALVALchain AAA1 - 2692 - 270
21ARGARGVALVALchain CCC1 - 2692 - 270
12METMETARGARGchain BBB0 - 971 - 98
22METMETASPASPchain FFF0 - 981 - 99
13GLUGLUSERSERchain DDD1 - 1991 - 199
23ASPASPPROPROchain GGG2 - 1982 - 198
14VALVALALAALAchain EEE2 - 2422 - 242
24VALVALTRPTRPchain HHH4 - 2394 - 239

NCSアンサンブル:
ID
1
2
3
4

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要素

#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 MAV36 TCR Alpha Chain


分子量: 22577.229 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 MAV36 TCR Beta Chain


分子量: 27901.236 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)
#5: 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
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: 2.57 Å3/Da / 溶媒含有率: 52.15 %
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
Reflection冗長度: 2.9 % / 数: 72832 / Rmerge(I) obs: 0.215 / D res high: 3.4 Å / D res low: 89.24 Å / Num. obs: 25456 / % possible obs: 97.4 / Rejects: 24
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)IDRmerge(I) obsRedundancy
3.43.6310.7112.9
9.6189.2410.0633
反射解像度: 3.4→89.24 Å / Num. obs: 25456 / % possible obs: 97.4 % / 冗長度: 2.9 % / Biso Wilson estimate: 71.95 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.149 / Net I/σ(I): 14 / Num. measured all: 72832 / Scaling rejects: 24
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.4-3.632.90.7113.41332946230.6470.49397.4
9.61-89.2430.06358.5346911440.9890.04396.6

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation3.4 Å89.24 Å
Translation3.4 Å89.24 Å

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解析

ソフトウェア
名称バージョン分類
Aimless0.5.7データスケーリング
PHASER2.5.7位相決定
PHENIX(phenix.refine: 1.9_1692)精密化
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: 3.4→48.715 Å / SU ML: 0.52 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 37.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3369 1274 5.03 %
Rwork0.2802 24073 -
obs0.2831 25347 97.22 %
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: 214.8 Å2 / Biso mean: 104.7627 Å2 / Biso min: 54.26 Å2
精密化ステップサイクル: final / 解像度: 3.4→48.715 Å
タンパク質核酸リガンド溶媒全体
原子数12530 0 44 0 12574
Biso mean--73.64 --
残基数----1550
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00512903
X-RAY DIFFRACTIONf_angle_d0.85217508
X-RAY DIFFRACTIONf_chiral_restr0.0351881
X-RAY DIFFRACTIONf_plane_restr0.0042264
X-RAY DIFFRACTIONf_dihedral_angle_d16.6494688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2083X-RAY DIFFRACTION13.08TORSIONAL
12C2083X-RAY DIFFRACTION13.08TORSIONAL
21B905X-RAY DIFFRACTION13.08TORSIONAL
22F905X-RAY DIFFRACTION13.08TORSIONAL
31D1558X-RAY DIFFRACTION13.08TORSIONAL
32G1558X-RAY DIFFRACTION13.08TORSIONAL
41E1959X-RAY DIFFRACTION13.08TORSIONAL
42H1959X-RAY DIFFRACTION13.08TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.53610.4061340.37092708284298
3.5361-3.6970.39381580.35082657281598
3.697-3.89180.34471380.32912686282498
3.8918-4.13560.38781500.31282680283098
4.1356-4.45470.30521210.27552709283098
4.4547-4.90260.30241330.25362703283698
4.9026-5.61110.31421410.26512690283198
5.6111-7.0660.35791520.27942582273494
7.066-48.72010.29761470.21882658280596
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)
12.51010.13440.84571.8613-0.58111.75620.0976-0.18120.6946-0.0330.3252-0.0992-0.45090.1593-0.14630.77720.00840.19020.4985-0.23720.794897.5703-41.021631.8016
22.2241-0.1097-0.35391.8575-0.12143.18280.0609-0.05160.09550.24310.3555-1.8443-0.30970.5599-0.38420.7585-0.02870.08410.6126-0.22181.5837106.5069-4536.4495
31.720.16570.55482.22550.02152.07870.53460.0340.7413-0.8086-0.1467-0.924-0.5455-0.1582-0.10391.00950.16290.48860.6512-0.0509196.4166-46.847224.6264
41.6374-0.0344-0.33432.71370.5591.52640.24990.1682-0.2737-0.2762-0.22860.8899-0.3219-0.44420.02750.62940.0889-0.04110.6811-0.22591.117584.1947-52.690531.0953
53.9529-1.1714-1.61743.0569-1.23154.99020.2607-0.3001-0.33640.25040.7059-0.99730.60380.4367-0.54360.86010.1163-0.09030.4059-0.12860.7941100.2794-55.975544.8205
62.1023-0.5229-0.6972.8070.90212.52370.4498-0.5157-0.1297-0.6147-0.1398-0.0571-0.48010.1213-0.27350.683-0.191-0.12040.69440.01630.714594.7032-27.683758.5719
72.5632-0.4536-0.98511.63910.13363.30110.3911-0.7914-0.1404-0.1558-0.0671-0.3745-0.2442-0.2873-0.2260.6173-0.08930.08060.7557-0.09410.725487.3708-26.485858.2541
81.3222-0.22740.2252.49641.22131.32910.2565-1.1651-0.6302-0.3633-0.2565-0.16950.08680.6717-0.03810.3035-0.6488-0.24951.40790.14050.392890.4929-26.790662.9059
94.31332.41371.54982.88031.57282.3941-0.05870.1316-0.39180.0967-0.04930.0870.4019-0.60490.10230.6182-0.04270.58230.61720.22881.57886.3126-28.387429.0776
100.30110.1392-0.1970.5174-0.05270.13880.1562-0.3249-0.320.2296-0.26730.08280.058-0.149-0.39590.8034-0.2810.4306-0.30160.54041.316996.1975-22.444744.8612
110.2550.6793-0.26581.791-0.67390.27460.0499-0.66710.24720.29330.0648-0.1268-0.47590.2109-0.05441.2165-0.20670.31781.11170.07230.8543106.9665-19.294256.2559
121.0804-0.4796-0.7110.49190.30070.4502-0.0533-0.2829-0.23850.1623-0.17760.1290.15460.178-0.39860.12550.58431.13120.3907-0.24720.7049100.9562-24.901843.6992
130.2290.24250.1420.37540.42920.6409-0.29910.65050.1825-0.5819-0.0074-0.1908-0.11020.14450.11931.0981-0.63911.0160.01990.61291.2819100.0736-22.918532.4608
141.0767-0.15110.36390.45280.50550.88490.5621-0.0461-0.18970.31290.2146-0.0452-0.67710.4925-0.4340.9363-0.0880.48130.6049-0.03291.532109.3398-19.391337.4666
151.1-0.04760.35071.9376-0.03691.21210.49190.46210.52730.1854-0.079-1.3477-0.1870.2711-0.16340.7992-0.00270.24680.5156-0.01161.0869101.1719-25.79841.6325
162.58352.3993.83332.24593.57445.6825-0.0807-0.0193-0.0684-0.103-0.0001-0.2807-0.19920.3420.19441.43070.05220.77820.33630.45631.3457100.5613-16.661436.7153
170.80630.0713-0.37230.3307-0.24211.1493-0.03380.11910.1275-0.10090.1016-0.0214-0.32340.2442-0.24471.17920.1650.88740.5476-0.11920.624192.0079-18.942528.2853
180.6565-0.34190.52130.51910.03060.70110.0513-0.20790.434-0.55920.03-0.1168-0.4027-0.22990.04491.1821-0.02950.32630.7283-0.12020.587396.9288-14.588343.6499
190.316-0.3991-0.33941.2343-0.35931.15330.56450.4346-0.5411-0.59080.3328-0.25860.28710.97220.03080.81090.0471-0.26630.8874-0.64570.6917128.3829-20.054617.8786
202.28880.63990.60221.48290.23511.68260.33720.1852-1.12530.25170.29360.69920.4661-0.1006-0.25410.6028-0.0311-0.34220.66650.07561.3993119.1673-22.98123.3885
211.79620.2597-0.05941.424-0.3920.1050.19990.2354-1.5151-0.6417-0.27751.0056-0.1507-0.75370.19220.8720.1545-0.41270.8826-0.14461.2688112.765-16.162612.9522
220.38730.89130.37121.90650.74142.3970.09160.316-0.22780.0801-0.2248-0.0368-0.02640.3692-0.21460.95820.3272-0.29530.9246-0.62751.0201122.1439-21.48686.8031
230.88460.07410.61310.47870.12841.3805-0.26650.221-0.0778-0.29360.09340.39690.32470.18350.18591.27440.10370.12451.211-0.16491.0046130.8755-14.07735.9865
240.0199-0.0917-0.13691.75650.40430.74280.59990.378-0.1205-0.9676-0.5760.04460.2670.18850.02330.76430.1764-0.23221.3623-0.22740.702123.745-6.39314.402
252.3855-0.8102-0.77121.0584-0.56251.8699-0.376-0.0747-0.0620.39830.6789-0.1635-0.53370.345-0.42970.5667-0.0733-0.18040.67840.01340.5041133.8756-16.358329.4735
262.2985-0.757-1.01150.25910.29020.76830.57370.4970.3635-1.1435-0.0496-0.50790.28750.3817-0.23441.14340.6996-0.5740.5576-0.63661.8718147.8847-35.687822.1363
271.09990.3281-0.08311.2279-0.33450.10120.91730.0555-0.9149-1.0769-0.211-0.28581.05160.1834-0.13211.0190.2076-1.10511.0517-0.10041.4504144.1393-36.937818.5038
282.30990.3681-2.92982.4713-1.40364.0854-1.01580.6272-0.3199-0.6809-0.4485-0.78680.33640.34020.26810.51970.1935-0.13671.7311-0.4791.2331155.4236-36.168220.1417
290.66050.111-0.10770.82170.28830.3123-0.38850.05190.6569-0.23680.22030.4468-0.38990.2269-0.01910.7295-0.19260.11720.70670.5943-0.2038112.643911.204317.0383
300.5433-0.04180.45973.3287-0.37880.4795-0.2848-0.0830.4822-0.01320.13310.7275-0.132-0.2333-0.02270.7289-0.0841-0.31770.54910.42560.2823105.852311.567716.2732
311.8567-1.7897-0.66591.73160.57622.3262-0.13310.19650.1367-0.2212-0.3726-0.1757-0.1034-0.38250.27331.11190.1686-0.43050.6777-0.11411.15387.293636.10917.2254
320.6255-0.0460.30510.61630.26560.2816-0.6389-0.82440.4812-0.0896-0.4356-0.0035-0.3897-0.2060.44010.87570.167-0.27891.2357-0.26411.05588.034529.710526.7278
332.6795-0.53120.32052.56380.77831.2654-0.2607-0.04110.5871-1.0236-0.11120.15570.4196-0.55150.18890.99470.1506-0.23990.9273-0.35670.56687.177429.17615.1541
340.96870.870.06212.66460.41470.3623-0.0391-0.324-0.09180.5235-0.13030.39410.0986-0.44710.26591.4155-0.22540.58091.5503-1.07091.611773.565132.158129.5156
352.26480.00570.51763.1276-0.52292.8436-0.4336-0.7161-0.01910.418-0.1460.4901-0.7017-0.15040.211.3076-0.0897-0.07591.206-0.37231.229484.848739.447726.1483
362.8318-0.21880.1132.31210.18161.87320.5020.2019-0.1351-0.17980.02670.47070.3829-0.1658-0.48950.7301-0.0179-0.21270.68630.10360.906592.295-3.5749.5526
373.8983-0.3477-0.23523.2972-0.94611.38260.5768-0.1423-1.31780.1368-0.76050.03230.13550.25560.10880.6709-0.0127-0.13050.63220.1610.70799.253-10.580813.4601
383.99670.9331-1.06382.99960.75792.182-0.14590.5355-0.2690.38790.35861.09920.619-0.07770.11320.6137-0.132-0.15850.68590.33260.712196.6102-5.730113.1052
393.4911-0.7242-1.10951.38710.41941.6754-0.5071-0.17590.30110.54240.50030.03220.52680.0098-0.0130.6294-0.0567-0.12590.89150.13480.665483.88412.08217.629
401.6606-0.3241-0.54252.38150.17871.2087-0.1764-0.16950.4433-0.6323-0.77820.4747-0.6303-0.27040.64080.68750.1716-0.32260.8118-0.0940.831478.064725.580412.3339
411.1726-0.02790.51221.38950.10240.3441-0.7631-0.044-0.56460.3777-0.20960.87940.3527-0.41040.371.09350.38580.15111.3312-0.04130.711482.249517.720717.3295
422.4661-1.41181.17342.2737-0.26252.3171-0.48760.61091.1334-0.232-0.62020.5092-0.50260.2070.62770.868-0.047-0.34790.94860.01420.857179.952529.32459.0997
431.9994-0.0563-2.19830.14740.41473.3995-0.8104-0.26690.2792-0.2483-0.5540.60880.4357-0.6127-0.43170.7685-0.2223-0.56280.94260.10671.164973.170511.99127.98
441.0995-0.8777-0.90410.70240.70810.7495-0.4564-0.0417-0.27620.3249-0.85470.40670.169-0.62840.42550.705-0.1225-0.57131.38840.03411.353768.682214.398410.6669
450.12280.0060.03170.0479-0.0460.05130.330.36020.5398-0.171-0.04630.06480.031-0.0142-0.05392.07670.5804-0.03261.5877-0.36480.8818126.4506-34.65411.7251
460.06770.1214-0.17310.2123-0.29560.41540.02850.1523-0.2117-0.04640.0904-0.2017-0.21590.03560.11582.2502-0.2841-0.1330.8166-0.3571.2338134.2709-42.817417.4343
470.0663-0.13610.03380.3322-0.15240.1710.1073-0.1733-0.0720.0788-0.2005-0.02330.0038-0.05680.0851.70640.2081-0.73580.9208-0.58232.219138.0739-48.275632.5644
482.26-0.1216-0.00861.70420.540.1636-0.2885-0.09850.02410.2271-1.0296-0.2862-0.2671-0.12040.47181.305-0.2094-0.3460.8074-0.10021.0089130.3711-40.654320.0327
491.2213-0.03170.17370.66350.57880.7328-0.650.9471-0.1921-0.1839-0.69660.3682-0.514-0.0610.55171.752-0.0310.18091.1490.13920.9848121.8868-42.698914.2209
501.16650.2839-0.11420.0683-0.07581.2792-0.14150.420.1131-0.08560.104-0.23190.0843-0.3202-0.01191.2208-0.0330.15450.9982-0.07231.8041121.1252-48.771624.3919
511.6146-0.0880.62831.10140.46030.50630.7707-0.5445-0.3798-0.43660.3555-0.24950.03340.1133-0.30070.98980.2781-0.2021.3163-0.09971.2425127.3904-27.680813.9041
520.67510.3182-0.69332.0708-0.66921.2905-0.4994-0.4434-0.03290.1026-0.95980.0538-0.3251-0.53470.73331.19410.1564-0.4050.7719-0.24311.5931128.5899-47.369322.0877
530.02620.0242-0.01730.0935-0.06580.04780.0450.3728-0.2041-0.35650.09360.02760.27740.0880.00022.21410.1331-0.69951.1502-0.54081.0389122.8408-44.86044.3895
541.89561.2837-0.0122.37121.02772.290.2974-0.4613-0.1570.3506-0.37510.0538-0.0870.6875-0.00261.52320.4050.06231.3736-0.27571.5092134.9328-51.027417.5284
550.9284-0.3339-0.2682.45690.00520.9485-0.06160.1702-0.0199-0.12820.2467-0.1287-0.04910.0861-0.24130.5036-0.01180.07090.595-0.16060.572599.6505-77.333422.6721
562.20920.0086-1.30680.7683-0.14752.2156-0.1951-0.1722-0.2882-1.0871-0.11080.48350.3480.1890.09321.4995-0.00930.47940.8727-0.2851.5036110.4651-102.30251.9807
570.5325-0.2904-0.23142.1845-0.15551.69180.023-0.44810.6966-1.42090.3923-1.1247-0.03260.4904-0.32151.5342-0.12080.49751.1313-0.35921.7947114.1767-100.46031.8409
580.9377-0.78050.85951.6540.26261.7464-1.09561.4552-0.3918-0.64580.061-0.9383-0.8391-0.22110.14262.11440.01910.94011.10350.00451.445105.1919-61.27591.7571
592.35991.24580.72711.197-0.03180.58050.7095-0.0909-0.1781-1.00150.0488-1.2714-1.01970.12850.35191.6769-0.0471.00260.7946-0.15371.1785105.9158-59.484610.6175
600.3362-0.2462-0.30530.23710.38930.8189-0.21810.42130.8548-0.25190.2378-0.38810.25480.1425-0.02472.3831-0.27650.37561.4663-0.14512.4699118.0692-81.1629-7.5473
610.4272-0.3282-0.09440.341-0.15840.61560.5890.1347-0.3518-0.1360.50130.33460.17450.2374-0.3742.32290.14910.36121.13520.22061.7095106.5601-100.7197-6.9887
620.0636-0.12530.06250.5893-0.59140.71920.52250.11270.4135-0.23080.39860.0521-0.27580.2605-0.28252.40860.41390.39021.386-0.55721.4672105.7-84.0087-6.562
631.15710.1917-0.35420.2580.20850.47490.05570.17420.0425-0.114-0.1211-0.2361-0.3086-0.0316-0.36291.814-0.28761.44771.471-0.39582.2295122.8417-82.92811.5087
640.5560.30070.59140.1960.22310.56970.83930.97410.0274-0.0375-0.1313-0.1202-0.28790.1883-0.32062.34870.0040.9331.5263-0.51232.1113109.3296-83.1043-13.6542
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 21 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 55 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 100 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 158 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 171 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 215 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 237 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 269 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 5 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 11 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 12 through 19 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 20 through 30 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 31 through 41 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 42 through 52 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 53 through 77 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 78 through 83 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 84 through 90 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 91 through 97 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 12 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 13 through 55 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 56 through 84 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 85 through 100 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 101 through 133 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 134 through 158 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 159 through 182 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 183 through 216 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 217 through 242 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 243 through 269 )C0
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 76 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 77 through 108 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 109 through 135 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 136 through 150 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 151 through 175 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 176 through 185 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 186 through 199 )D0
36X-RAY DIFFRACTION36chain 'E' and (resid 2 through 38 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 39 through 72 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 73 through 101 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 102 through 122 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 123 through 160 )E0
41X-RAY DIFFRACTION41chain 'E' and (resid 161 through 186 )E0
42X-RAY DIFFRACTION42chain 'E' and (resid 187 through 201 )E0
43X-RAY DIFFRACTION43chain 'E' and (resid 202 through 223 )E0
44X-RAY DIFFRACTION44chain 'E' and (resid 224 through 242 )E0
45X-RAY DIFFRACTION45chain 'F' and (resid 0 through 5 )F0
46X-RAY DIFFRACTION46chain 'F' and (resid 6 through 11 )F0
47X-RAY DIFFRACTION47chain 'F' and (resid 12 through 20 )F0
48X-RAY DIFFRACTION48chain 'F' and (resid 21 through 30 )F0
49X-RAY DIFFRACTION49chain 'F' and (resid 31 through 41 )F0
50X-RAY DIFFRACTION50chain 'F' and (resid 42 through 51 )F0
51X-RAY DIFFRACTION51chain 'F' and (resid 52 through 61 )F0
52X-RAY DIFFRACTION52chain 'F' and (resid 62 through 83 )F0
53X-RAY DIFFRACTION53chain 'F' and (resid 84 through 90 )F0
54X-RAY DIFFRACTION54chain 'F' and (resid 91 through 98 )F0
55X-RAY DIFFRACTION55chain 'G' and (resid 2 through 108 )G0
56X-RAY DIFFRACTION56chain 'G' and (resid 109 through 145 )G0
57X-RAY DIFFRACTION57chain 'G' and (resid 146 through 198 )G0
58X-RAY DIFFRACTION58chain 'H' and (resid 4 through 34 )H0
59X-RAY DIFFRACTION59chain 'H' and (resid 35 through 108 )H0
60X-RAY DIFFRACTION60chain 'H' and (resid 109 through 132 )H0
61X-RAY DIFFRACTION61chain 'H' and (resid 133 through 147 )H0
62X-RAY DIFFRACTION62chain 'H' and (resid 148 through 171 )H0
63X-RAY DIFFRACTION63chain 'H' and (resid 172 through 188 )H0
64X-RAY DIFFRACTION64chain 'H' and (resid 189 through 239 )H0

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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