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- PDB-6pum: Structure of human MAIT A-F7 TCR in complex with human MR1-2'D-5-OP-RU -

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基本情報

登録情報
データベース: PDB / ID: 6pum
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-2'D-5-OP-RU
要素
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha chain
  • TCR beta chain
キーワードIMMUNE SYSTEM / MAIT / MR1 / Metablite presentation
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-Q84 / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.96 Å
データ登録者Awad, W. / Keller, A.N. / 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) オーストラリア
引用ジャーナル: Nat.Immunol. / 年: 2020
タイトル: The molecular basis underpinning the potency and specificity of MAIT cell antigens.
著者: Awad, W. / Ler, G.J.M. / Xu, W. / Keller, A.N. / Mak, J.Y.W. / Lim, X.Y. / Liu, L. / Eckle, S.B.G. / Le Nours, J. / McCluskey, J. / Corbett, A.J. / Fairlie, D.P. / Rossjohn, J.
履歴
登録2019年7月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年2月19日Provider: repository / タイプ: Initial release
改定 1.12020年3月11日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
改定 1.22020年3月18日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.32020年4月1日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.42023年10月11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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id
改定 1.52024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: TCR alpha chain
E: TCR beta chain
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)189,37320
ポリマ－188,1008
非ポリマー1,27312
水26,7881487
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,61810
ポリマ－94,0504
非ポリマー5676
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: TCR alpha chain
E: TCR beta chain
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,75610
ポリマ－94,0504
非ポリマー7066
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)218.055, 70.242, 144.022
Angle α, β, γ (deg.)90.000, 104.570, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

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タンパク質 , 4種, 8分子 ACBFDGEH

#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 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MR1 / 発現宿主: Escherichia coli (大腸菌) / 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 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769
#3: タンパク質 TCR alpha chain


分子量: 22781.268 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#4: タンパク質 TCR beta chain


分子量: 27677.760 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)

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非ポリマー , 4種, 1499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: 6 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物 ChemComp-Q84 / 1,2-dideoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-erythro-pentitol


分子量: 314.295 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C12H18N4O6 / タイプ: SUBJECT OF INVESTIGATION
#7: 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: 4 / 由来タイプ: 合成 / 式: Na
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1487 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.84 Å3/Da / 溶媒含有率: 56.65 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 100 mM BTP (pH 6.0 - 6.5), 8-20% PEG3350 and 200 mM sodium acetate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
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: 0.95365 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年10月4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: 0.95365 Å / 相対比: 1
反射解像度: 1.96→48.32 Å / Num. obs: 150402 / % possible obs: 99.17 % / 冗長度: 3.7 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.11
反射 シェル解像度: 1.96→2.03 Å / Num. unique obs: 14877 / CC1/2: 0.665

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
XDSデータ削減
pointlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4L4T

4l4t


解像度: 1.96→48.32 Å / SU ML: 0.193 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 20.6322
Rfactor反射数%反射
Rfree0.1896 7542 5.02 %
Rwork0.1539 --
obs0.1557 150360 99.18 %
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 mean: 47.71 Å2
精密化ステップサイクル: LAST / 解像度: 1.96→48.32 Å
タンパク質核酸リガンド溶媒全体
原子数12740 0 82 1487 14309
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.010113636
X-RAY DIFFRACTIONf_angle_d1.036818649
X-RAY DIFFRACTIONf_chiral_restr0.06682001
X-RAY DIFFRACTIONf_plane_restr0.0072448
X-RAY DIFFRACTIONf_dihedral_angle_d16.51298262
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.33052670.28084672X-RAY DIFFRACTION98.37
1.98-2.010.29082510.24664758X-RAY DIFFRACTION98.7
2.01-2.030.27632490.24064675X-RAY DIFFRACTION98.42
2.03-2.060.23682290.22674752X-RAY DIFFRACTION98.65
2.06-2.080.25512440.20564722X-RAY DIFFRACTION98.71
2.08-2.110.24352370.20214652X-RAY DIFFRACTION98.77
2.11-2.140.23142390.18914741X-RAY DIFFRACTION98.89
2.14-2.170.22622370.18684729X-RAY DIFFRACTION99.12
2.17-2.210.21462500.1794793X-RAY DIFFRACTION99.15
2.21-2.240.23092590.17524703X-RAY DIFFRACTION99.18
2.24-2.280.24082330.17254751X-RAY DIFFRACTION99.24
2.28-2.320.20642480.17294750X-RAY DIFFRACTION99.25
2.32-2.370.2362590.17514746X-RAY DIFFRACTION99.25
2.37-2.420.21862520.1694700X-RAY DIFFRACTION99.46
2.42-2.470.21472490.17224767X-RAY DIFFRACTION99.43
2.47-2.530.23492640.17284766X-RAY DIFFRACTION99.39
2.53-2.590.22862550.16934768X-RAY DIFFRACTION99.35
2.59-2.660.2032600.16654749X-RAY DIFFRACTION99.52
2.66-2.740.22512510.15864747X-RAY DIFFRACTION99.54
2.74-2.830.2232460.16824810X-RAY DIFFRACTION99.68
2.83-2.930.2212430.16424786X-RAY DIFFRACTION99.54
2.93-3.040.19862520.15924766X-RAY DIFFRACTION99.39
3.04-3.180.19182460.15394796X-RAY DIFFRACTION99.45
3.18-3.350.18152620.14994781X-RAY DIFFRACTION99.19
3.35-3.560.18562400.13674775X-RAY DIFFRACTION99.6
3.56-3.840.16822430.12984814X-RAY DIFFRACTION99.59
3.84-4.220.14512610.12494809X-RAY DIFFRACTION99.59
4.22-4.830.13022630.10844802X-RAY DIFFRACTION99.59
4.83-6.090.15782720.1364837X-RAY DIFFRACTION99.05
6.09-48.340.19172810.17094901X-RAY DIFFRACTION98.4
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)
12.353866499920.32378985944-0.156448318611.99103518182-0.9930608235912.119319217350.00421169550511-0.1181411844480.239832551610.09644694424130.07286801800440.195326389704-0.019649398418-0.258689669332-0.07591145520820.203878869930.036271635478-0.01098714319980.2818150837270.01098083759550.31417047614-49.116014194938.9858809734193.210809297
21.9571449572-0.170844641817-0.3715475839913.714105442310.09752989398321.322498570620.01282434147240.126027145740.274470224742-0.176904877825-0.0191073714685-0.427626450394-0.1148769018510.08734685204080.01500958259790.238055077925-0.00614204562741-0.00336552283760.2434280592580.03897523705930.330887035024-36.86119767342.4822623991182.392784398
33.50876379423-0.4144233465951.730435609831.30539908671-0.426810688682.466520648910.0940951911118-0.00510313302157-0.196716193911-0.1789430485380.1833749050230.3490998606180.150434670983-0.467246901547-0.2686240558780.314120010387-0.085586107921-0.04051724728510.3910756246030.06424364519030.320007442762-62.18183183132.098471303174.02192234
41.81671584253-0.6321674961080.3560865004262.309871912610.2579923654192.25829828909-0.02361707161270.4006788149260.48695849388-0.504201948504-0.0148118118561-0.00134172575383-0.384066053922-0.02749427210430.06550230277280.421530110789-0.107956813683-0.07537199106020.684218093980.1959051809590.50736589923-66.86334277941.5085561795160.715294349
53.89734520891-0.274266679713-0.1941951149422.383528202720.1395438532132.33591575337-0.2970543080470.1613632418190.625564479982-0.2714296239760.252324276520.532267940264-0.0605876517601-0.5661486996410.05646767826790.3368826585710.0511231331569-0.09308168984430.5740949629260.1375148765920.587846122865-68.345502449848.8933823934179.367921648
62.003105341520.2548396798050.4972557244580.5074571546230.04752099467580.5807769561470.0225403124982-0.3809641916050.487108485630.2539547424630.00569951765880.56803003119-0.252080527921-0.623629635456-0.02783465987180.3661475441130.124541171034-0.01559887130970.60141519536-0.00146032260540.769629059738-65.04196056454.5674271773187.71701945
79.57368794066-4.689179455350.07729116784022.54194408599-0.3737724842421.39043577273-0.566090483481-1.13724132192-0.2651912327240.2986445738120.3863439847290.769286711817-0.304108780493-0.8904185526730.149357041310.3673450467030.107693641933-0.01567919541780.8308580152790.01554670571150.665389612015-69.332881903748.6627227915189.447283352
82.039027699970.2889571716650.1490349066031.239934135930.2021388378511.33332877046-0.116126564923-0.34660822462-0.04673719953640.03024945667140.05221203412360.2876803033010.0298494224579-0.5945641071680.1171097668520.2798157833480.0229760611264-0.0306899709470.479955115420.0643529707610.443688655236-63.761750920246.2672341631183.54988859
95.58253057430.01362690997570.8193126376291.47023613134-0.1736908995332.03484203971-0.1420988543680.1611567864891.1723620851-0.1911822474110.1032561621670.902211478314-0.537095918591-0.8745573651760.07578502110190.4020348720610.151212795172-0.1228650492830.7120999349110.01056733970020.959514212274-72.620949497456.884520179181.482754146
101.220889069990.349721678549-0.2006046953183.133103955510.5158609676042.25910940220.0111651366197-0.390231864162-0.05153157215680.21883398433-0.130319791303-0.193456706864-0.08934908890270.07020277250020.1110630620480.240452153360.02737386686140.01264687006380.4535495165650.0488731217650.2588211967655.8645496810524.541031426256.669544536
111.30817068485-0.116205167736-0.2540621276512.271380134630.9497574550661.189021434050.0246421702523-0.10340336851-0.0702913995084-0.216191703017-0.1878623295310.02172783468540.0478175830463-0.1883089685970.1579837830210.2517755801220.04434339382760.02904058810250.3764231481770.04689361936710.205238598357-2.2834646541117.5992748788246.372603032
122.42387689649-1.11594396574-0.7282722307931.22191875170.6362716811811.477620412240.05259142315930.04799729771690.1044473952120.0511191581818-0.022764047595-0.205690091751-0.1954297821170.0446597697393-0.01864538489580.4375257653360.0005308293927270.04022648361490.1977612842410.02800441984190.36519654725421.288409249935.4745053858228.284140407
132.374922102520.1165873978560.8197185609552.29155179941-0.4019838938442.467072320680.02577626836460.330469191217-0.152084492032-0.2423761041470.0610662492573-0.1262686030910.06598148027230.217149130135-0.05582720260990.309919253926-0.01470694677340.04257186940550.1810282913350.001614344558220.32280535736221.56298246232.4460125298223.142376335
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152.044758383731.56408074726-3.994083974380.774823140398-0.876832935352.24985033909-0.09615526730230.5937503660310.111380311531-0.004212574788240.1437692772620.4674910643760.321456679251-0.866764662624-0.04534227167580.357265049015-0.01334022216280.007624412918860.828145827995-0.04490474413720.492309633809-49.741377396321.0920366062265.837906429
164.777957942260.7088004682371.254835570392.69983304005-0.2103650918174.33022708278-0.00411227466048-0.12754513020.8492703505430.1396185898980.04643557618060.500657253434-0.0660777441308-0.464280823489-0.08040656082250.504007784887-0.007265027139730.01987728895740.811064247032-0.03073128968750.744308930651-54.805115854724.691293865280.141541517
173.948829988280.6454717123070.3564914631842.067323464680.1100549200491.71856386304-0.111393556468-0.5340062453240.0928213669360.214872959234-0.1425105648220.0852148080904-0.132854309623-0.1124905150870.2324852481560.3344376665460.0923312230482-0.02013799708750.562111887696-0.07009565058640.218500624934-13.37318443823.0983780884276.321111228
181.596910784330.0881383646197-1.076447907761.182770729530.3585789157751.794544887760.261411922327-0.6123811473530.6398297015490.2381339043520.264027793678-0.117804345641-0.2512790577960.209564195966-0.4684851389740.4986374074230.08611570140670.07068299728110.962906151453-0.2261653902480.474136765623-27.502457040428.8462705968292.534622251
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212.018006309272.178900930793.264314261562.018382764172.434657340897.753090604620.0960572495954-0.753315949821-1.193478837450.52619962452-0.457483381698-0.01556765277460.909575792193-0.6135209294220.3952309216980.420828620880.01785425371750.08111647437290.3646015159940.09701354347890.56960935225520.588751535110.7082559339246.09692055
222.843260913330.104536909254-0.09994477634853.33144934351-1.013676397062.40421202376-0.0790858106774-0.1683912318450.59903834887-0.342342222805-0.138075003409-0.359014910755-0.4656448676790.3988067096790.1598869325990.372511408573-0.0560552102268-0.005397477058230.2780116422160.02690572911960.41668229363330.713489853535.2246994455239.679583771
233.24150938372.21762380661-0.2882483634946.33066527686-0.9966506697182.10254460236-0.11881742995-0.4013439579560.12360055439-0.139643619069-0.0326997085413-0.37889653875-0.3925354743680.07147094755140.1564951178820.3409564452860.0267355266385-0.01410544527530.241759406856-0.01022154701930.33354949353126.373903293930.3531383309244.66661652
242.159768022429.1281472154-0.84765052389910.0452098519-1.216332581023.09870770058-0.0690975121473-0.955083872906-0.2816925004020.7602141474980.0267368164926-0.589976186071-0.355591183101-0.01760390942860.01690796350360.3350625960050.0784163210361-0.09774633332040.3289229393250.05096466280530.5061886901727.723980319422.3256043692252.186742393
258.859609418661.121992584542.205907018262.64602956292-0.115111995931.73501741443-0.209978130632-0.6692220833180.3820982557740.661967043402-0.0511676842225-0.270931437637-0.3822729424150.2943994703040.2766058122950.467950278416-0.0203878991754-0.120969330520.546681426161-0.02658503207030.51820880839933.050343590232.0474153205254.096105601
263.3396632609-0.08245716494354.028924889184.140472771874.197295628489.313121038850.161473103001-0.2839093896030.111546360529-0.0569705545120.246163996168-0.1164398904920.217360235264-0.00730934182734-0.3613241755360.3611887354640.05817996429020.01882876800880.3927623304460.01726299605090.29005174740915.710472974226.0000355524251.256037509
278.36925811485.483596387290.07639582754316.01818279492-0.5586564458922.05843433302-0.195378847679-0.2889779873580.4369544680230.03380346360660.1633392120590.285790821931-0.2030886233510.007723773091950.03241432933050.2798472747370.05747947471020.04529405047510.2384993412870.01305154799380.25335147866221.642917721427.729125345247.021844085
280.4374219435890.495464457031-0.2361430742630.554498246241-0.2662544962640.1289052215870.0396110832113-0.01521656454880.765749707975-0.0130739681219-0.291949264783-0.31355407847-0.1908938223250.4187644610420.2323547337410.439633773042-0.0800282447407-0.01929759642180.4699470264220.0633357555961.0492130198742.929929739336.5499692783243.104681747
296.650025857044.311103544960.03104384102427.44411688387-0.3536637749473.58658490169-0.0811122137204-0.549345281870.1343318343140.6310110918270.157341973134-0.2375968459270.092062231982-0.1319434685550.007258379779420.3238739599450.0496726702287-0.04484128187110.3003178439440.04955841563740.32526328855632.599523307623.2322968843249.26768324
301.545517354023.490574996661.759926891382.005391567670.008326091380897.58323474933-0.1942792990040.0491726664517-0.4783877843880.14983953766-0.104235542527-0.835187792520.2540338761490.8605435120980.2445024650070.3920135520870.0691877200342-0.005280113287240.4141046529590.153685497780.48013660579431.475052295812.6876331112250.208277089
316.743297393551.87204129427-0.5179421723972.05008443195-3.324153225136.87740207597-0.15307308710.5969033285770.383792179497-0.2508825747190.156481433382-0.333818343925-0.3642267714850.43148675416-0.1185611606840.32084268058-0.0267549398230.007984988513120.3991284703950.04407492416530.41521841319936.326172853927.6138539264240.607137609
322.11613541059-1.454128722550.6507723176312.02846497039-0.6037807010071.127183433490.00692101493899-0.0820070790524-0.103216700988-0.03404360413920.05187520156350.03153686421820.183542914693-0.0514414190914-0.06373646090980.2497801537840.01220912827820.01831987786660.157792520311-0.02099891896270.254198675332-23.008553718.5132563227195.492383916
338.591068441460.3604313048532.698278263081.46546519777-1.020640541643.30491100037-0.1107611621020.429981015613-0.0710666618403-0.04163467212190.0696431301931-0.182281440614-0.1741882492290.1700936161640.03966237582850.3040239510720.04993042584470.02531408468910.181589445251-0.01457748986210.274305442599-20.262618796820.309047964187.271403147
345.74544719286-1.480951842920.7956296154191.49640427472-0.06681231919431.29557750951-0.00854039791262-0.11253724270.224608010709-0.07304518311050.0739146847247-0.197820030191-0.05906190171660.0776206336311-0.02391623187740.3051227096540.03381885898580.005705047073340.149907436024-0.03254154183180.252757090323-15.96494123420.204359245197.818807866
354.51573873455-2.046063317162.025587162041.55208731581-0.9255684758141.228009639380.04768601737540.270710470187-0.200614251754-0.00399713258195-0.0451257319898-0.02397311979250.07492824935460.0907356438347-0.01380993554520.3014397336020.01817715997020.01169960384140.197612624965-0.03575487473610.235631216573-13.1170726714.0778950116203.012347608
361.51923843348-0.812472367436-2.084436421541.491066065511.192362772142.0535927435-0.227509826843-0.211724577886-0.2638737148330.308698701755-0.0754763238422-0.0428954123630.1472625312780.2991807503150.2678702315150.423213891420.02766925084720.01423978184460.2368847424740.03561426438930.3222562271682.58023583697.29218811738226.753094969
373.64299665346-1.05173872312-0.8660161159931.633309594720.1830970011015.825336360510.02269947734850.4008040557550.0816933000810.0493355502248-0.06788741286140.1216424513170.0983552908439-0.3393500615070.03254828743540.324557207870.03643973696050.006190187013460.208316567031-0.04930436554430.315302565559-1.769354529788.0642908913213.12096897
381.94108440199-0.515014993329-1.542730616381.346394368951.525197705759.34900396658-0.0362416678388-0.145680496203-0.7879310801350.8278366614320.07591641393450.0455911111711.84956862785-0.341678405905-0.06586214156130.695426795651-0.008384699656290.09104755147420.274409428120.006483983327610.56994743466-0.666755268794-3.49037959756221.912371192
397.281506206891.192872577013.042131219844.839374426632.152566912835.470755857830.389057192161-0.0403653787704-0.6428577347630.6715953387380.279917843398-0.5234224381910.6136177407880.467069748303-0.6265668254380.4382727426020.0763983781914-0.0090336836430.238903505582-0.05488793346820.4085621177699.84936916147-1.95254421229215.19007891
402.12476962066-0.3742248913550.3246203834613.88567818825-1.303331556183.49312586446-0.0963140595611-0.5427288267210.2865880526080.5375246391160.0165358772323-0.0849955809167-0.590538948548-0.148632255880.06623558730160.3351796911750.0864754002682-0.05045913869020.363005048008-0.06691656138060.279851550877-28.015098962328.8569496248221.086438112
412.75312337317-0.6977835639830.2396279734362.31215926959-1.492796809882.31858045415-0.103424163951-0.3204273739660.1552213406850.181641830920.1042661617980.0945227682251-0.205360346103-0.267720715323-0.003050866310330.2577683537770.0680246200868-0.01422134099460.285761364026-0.06100742119090.23306523073-34.600188597728.627435037212.202905198
421.00018808421-0.105379572641-0.6960810443211.98800724058-0.2137334020590.841302600226-0.07463942567510.188207515890.0366119111548-0.1170296018520.00136670924813-0.106595053654-0.162964351945-0.1792090010540.0528383005890.3142484962210.0435165474588-0.02357204590760.221791041037-0.05229223282080.305316893535-29.052600903633.0312555721200.98097031
432.70957681611-0.8930523467511.796356829011.19399096183-0.3457624613591.536375659550.1171326520420.128480363653-0.345302107556-0.102874396247-0.0407153359190.02713849178550.208873258539-0.292392781809-0.03299409670850.2903379912050.005789896125560.01202520346490.29563283129-0.03833014461660.282141766708-25.755149377415.2217763993229.066610047
442.904175530030.219473792397-0.7149674733360.8103411448260.6873511642991.323098498340.1064274057330.08074660436740.0904378170643-0.0209819839855-0.0616855883538-0.0259216951865-0.149336653188-0.0592342348063-0.04484771245610.291666126230.04695021094790.0180276670450.148253892790.006928617065540.223778749771-0.9355931892915.211865552223.066747617
453.06619792536-0.557187095141-0.6297660970832.4046853310.06211525182423.374813467460.08927631661880.4387105820740.16197988068-0.130175263339-0.06385138397150.375533830209-0.0580012203932-0.398204831319-0.00865839243870.3467104727330.0889034583506-0.009358410534910.260890623872-0.01878524254930.278096773419-10.271669818514.27706707220.61876603
462.444259709890.321816318059-2.061477393840.866016219478-0.5222694377551.899702435920.2354191179870.2722382582040.006555512269170.112266168643-0.0906162817547-0.135236507463-0.342384848109-0.0933041950398-0.10991350560.4154005985220.02202844102680.02379258965740.19160105741-0.0182603943830.3000068692252.9339492032916.7729361993219.754143716
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485.276321646570.539692285367-1.689463605391.02805390156-0.02565338548081.9698857810.203034007311-0.240526703260.1656201835230.0181032691083-0.1212555885280.0599797473385-0.133827165371-0.137272528325-0.07099710818810.3354158247390.0480461342889-0.02997042591040.258086011914-0.03023876195150.215584501663-14.318882738120.4624659467234.995714747
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 205 )
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 97 )
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 84 )
11X-RAY DIFFRACTION11chain 'C' and (resid 85 through 171 )
12X-RAY DIFFRACTION12chain 'C' and (resid 172 through 216 )
13X-RAY DIFFRACTION13chain 'C' and (resid 217 through 270 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 102 )
15X-RAY DIFFRACTION15chain 'D' and (resid 103 through 116 )
16X-RAY DIFFRACTION16chain 'D' and (resid 117 through 199 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3 through 109 )
18X-RAY DIFFRACTION18chain 'E' and (resid 110 through 124 )
19X-RAY DIFFRACTION19chain 'E' and (resid 125 through 203 )
20X-RAY DIFFRACTION20chain 'E' and (resid 204 through 244 )
21X-RAY DIFFRACTION21chain 'F' and (resid 0 through 5 )
22X-RAY DIFFRACTION22chain 'F' and (resid 6 through 19 )
23X-RAY DIFFRACTION23chain 'F' and (resid 20 through 30 )
24X-RAY DIFFRACTION24chain 'F' and (resid 31 through 41 )
25X-RAY DIFFRACTION25chain 'F' and (resid 42 through 51 )
26X-RAY DIFFRACTION26chain 'F' and (resid 52 through 56 )
27X-RAY DIFFRACTION27chain 'F' and (resid 57 through 71 )
28X-RAY DIFFRACTION28chain 'F' and (resid 72 through 77 )
29X-RAY DIFFRACTION29chain 'F' and (resid 78 through 84 )
30X-RAY DIFFRACTION30chain 'F' and (resid 85 through 90 )
31X-RAY DIFFRACTION31chain 'F' and (resid 91 through 98 )
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 52 )
33X-RAY DIFFRACTION33chain 'G' and (resid 53 through 75 )
34X-RAY DIFFRACTION34chain 'G' and (resid 76 through 91 )
35X-RAY DIFFRACTION35chain 'G' and (resid 92 through 120 )
36X-RAY DIFFRACTION36chain 'G' and (resid 121 through 135 )
37X-RAY DIFFRACTION37chain 'G' and (resid 136 through 175 )
38X-RAY DIFFRACTION38chain 'G' and (resid 176 through 190 )
39X-RAY DIFFRACTION39chain 'G' and (resid 191 through 202 )
40X-RAY DIFFRACTION40chain 'H' and (resid 1 through 25 )
41X-RAY DIFFRACTION41chain 'H' and (resid 26 through 94 )
42X-RAY DIFFRACTION42chain 'H' and (resid 95 through 109 )
43X-RAY DIFFRACTION43chain 'H' and (resid 110 through 124 )
44X-RAY DIFFRACTION44chain 'H' and (resid 125 through 162 )
45X-RAY DIFFRACTION45chain 'H' and (resid 163 through 188 )
46X-RAY DIFFRACTION46chain 'H' and (resid 189 through 202 )
47X-RAY DIFFRACTION47chain 'H' and (resid 203 through 215 )
48X-RAY DIFFRACTION48chain 'H' and (resid 216 through 244 )

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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

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