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- PDB-6vmc: T4H2 T cell receptor bound to HLA-A2 presenting gp100T2L peptide ... -

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基本情報

登録情報
データベース: PDB / ID: 6vmc
タイトルT4H2 T cell receptor bound to HLA-A2 presenting gp100T2L peptide (ILDQVPFSV)
要素
  • (T4H2 T cell receptor ...) x 2
  • Beta-2-microglobulin
  • MHC class I antigen, A-2 alpha chain
  • Melanocyte protein PMEL
キーワードIMMUNE SYSTEM / TCR / MHC class I / HLA A2 / melanoma
機能・相同性
機能・相同性情報


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / antigen processing and presentation of peptide antigen via MHC class I / Regulation of MITF-M-dependent genes involved in pigmentation / : ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / antigen processing and presentation of peptide antigen via MHC class I / Regulation of MITF-M-dependent genes involved in pigmentation / : / : / 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 / lumenal side of endoplasmic reticulum membrane / 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 iron ion transport / regulation of erythrocyte differentiation / 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 / positive regulation of T cell activation / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / positive regulation of protein binding / 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / melanosome / DAP12 signaling / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / 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
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
類似検索 - ドメイン・相同性
Major histocompatibility complex, class I, A / MHC class I antigen / Melanocyte protein PMEL / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.85 Å
データ登録者Smith, A.R. / Baker, B.M.
資金援助1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2021
タイトル: Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner
著者: Smith, A.R. / Alonso, J.A. / Ayres, C.M. / Singh, N.K. / Hellman, L.M. / Baker, B.M.
履歴
登録2020年1月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年1月20日Provider: repository / タイプ: Initial release
改定 1.12021年1月27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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.22023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年10月30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
D: T4H2 T cell receptor alpha chain
E: T4H2 T cell receptor beta chain
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanocyte protein PMEL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,0396
ポリマ－94,9475
非ポリマー921
水23413
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanocyte protein PMEL
ヘテロ分子

D: T4H2 T cell receptor alpha chain
E: T4H2 T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)95,0396
ポリマ－94,9475
非ポリマー921
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation6_544x-y,x-1,z-1/31
Buried area10800 Å2
ΔGint-60 kcal/mol
Surface area38340 Å2
手法PISA
単位格子
Length a, b, c (Å)129.532, 129.532, 115.656
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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要素

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T4H2 T cell receptor ... , 2種, 2分子 DE

#1: タンパク質 T4H2 T cell receptor alpha chain


分子量: 22768.986 Da / 分子数: 1 / Mutation: 0 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRAV12-2, TRAC / プラスミド: pGMT7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): pLysS
#2: タンパク質 T4H2 T cell receptor beta chain


分子量: 27427.480 Da / 分子数: 1 / Mutation: 0 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRBV19, TRBC2 / プラスミド: pGMT7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): pLysS

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タンパク質 , 2種, 2分子 AB

#3: タンパク質 MHC class I antigen, A-2 alpha chain


分子量: 31854.203 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XL1-Blue / 参照: UniProt: A0A5B8RNS7, UniProt: A0A140T913*PLUS
#4: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 1 / 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: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XL1-Blue / 参照: UniProt: P61769

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タンパク質・ペプチド , 1種, 1分子 C

#5: タンパク質・ペプチド Melanocyte protein PMEL / ME20-M / ME20M / Melanocyte protein Pmel 17 / Melanocytes lineage-specific antigen GP100 / Melanoma- ...ME20-M / ME20M / Melanocyte protein Pmel 17 / Melanocytes lineage-specific antigen GP100 / Melanoma-associated ME20 antigen / P1 / P100 / Premelanosome protein / Silver locus protein homolog


分子量: 1017.175 Da / 分子数: 1 / Fragment: epitope (UNP residues 209-217) / Mutation: T210L / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P40967

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非ポリマー , 2種, 14分子

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


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 13 / 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N
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: 2.95 Å3/Da / 溶媒含有率: 58.3 %
結晶化温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 18% v/v PEG10000, 16% v/v glycerol, 250 mM Tris pH 8.5, 60 mM sodium chloride

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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: APS / ビームライン: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年6月18日
放射モノクロメーター: double crystal Si(111) / 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: 1.0332 Å / 相対比: 1
反射解像度: 2.85→50 Å / Num. obs: 25782 / % possible obs: 100 % / 冗長度: 19.8 % / Biso Wilson estimate: 50.79 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.045 / Rrim(I) all: 0.202 / Χ2: 1.015 / Net I/σ(I): 26
反射 シェル解像度: 2.85→2.9 Å / 冗長度: 14.9 % / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 3 / Num. unique obs: 1266 / CC1/2: 0.611 / CC star: 0.871 / Rpim(I) all: 0.316 / Rrim(I) all: 1.224 / Χ2: 0.979 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
PHENIX1.13_2998精密化
HKL-2000データ削減
HKL-2000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: PDB entry 1TVH

1tvh


解像度: 2.85→25.74 Å / SU ML: 0.4132 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.9733
Rfactor反射数%反射
Rfree0.2385 1997 7.8 %
Rwork0.197 --
obs0.2002 25615 99.55 %
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: 68.09 Å2
精密化ステップサイクル: LAST / 解像度: 2.85→25.74 Å
タンパク質核酸リガンド溶媒全体
原子数6642 0 6 13 6661
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00246830
X-RAY DIFFRACTIONf_angle_d0.44629277
X-RAY DIFFRACTIONf_chiral_restr0.0421965
X-RAY DIFFRACTIONf_plane_restr0.00291218
X-RAY DIFFRACTIONf_dihedral_angle_d18.10472510
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.38041340.28721592X-RAY DIFFRACTION95.78
2.92-30.31441450.2841691X-RAY DIFFRACTION99.51
3-3.090.29521440.27721685X-RAY DIFFRACTION100
3.09-3.190.31691430.25211674X-RAY DIFFRACTION100
3.19-3.30.31361470.23991696X-RAY DIFFRACTION100
3.3-3.440.25431450.22161683X-RAY DIFFRACTION100
3.44-3.590.25381470.21991702X-RAY DIFFRACTION100
3.59-3.780.24291390.20821686X-RAY DIFFRACTION100
3.78-4.020.23781370.19791697X-RAY DIFFRACTION100
4.02-4.320.21191390.17121698X-RAY DIFFRACTION100
4.32-4.760.17711450.14581701X-RAY DIFFRACTION100
4.76-5.440.19481490.15651694X-RAY DIFFRACTION100
5.44-6.830.23531380.1871709X-RAY DIFFRACTION100
6.83-25.740.20991450.16321710X-RAY DIFFRACTION98.46
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)
15.47005680437-0.7161541748720.8082856890351.921442309392.940452327625.181778758250.01697461889120.244758679477-1.36471349872-1.64577384170.4360394678790.6251061533690.793869430102-0.0578356333921-0.4830446887130.609786036583-0.202765927657-0.1356849060780.603703825117-0.1578705495510.81268735499186.5594654127-30.539287688219.2052442737
28.174034694291.319805203731.370640465434.471717483730.8721216670921.67814507169-0.28950591342-0.507103828787-1.0236680241-0.5365781973760.482875630064-0.2397267097920.611746569716-0.306253427362-0.1345484283190.457988405491-0.2293118359540.04131194549010.724367332362-0.06277595901930.42103026195687.4810410389-21.134113366927.0018162489
34.522069385494.39443675707-1.1021645224.55578128285-0.1874867054723.82622863329-0.5184105182380.507533943888-1.16815519393-0.3216168161030.58636725109-1.315617521530.635849316749-0.3213438552470.08149244346590.435075365626-0.1233198271760.0771100184420.658565902298-0.1047874634690.73666983644394.8005970435-27.511440891128.5129038687
46.274136371560.556224106377-1.370174886036.83817221012-2.478743459153.53395316251-0.11993898883-0.4908030831-0.4805072697230.06418274110320.04142301145750.5470447182860.215798667718-0.0562170602750.1309402943080.315082580143-0.1911810934080.06630063668090.602980205333-0.09038672009770.3627073442885.2658430765-22.60037753325.3843884998
55.857670691615.753742442270.5676756671055.728596896110.2874116230540.9697324466690.156015992084-0.11195576968-1.232222764660.0155562702862-0.323040059874-0.5453071618930.1783961801010.274903072771-0.05302171165161.04607396873-0.1687960213970.08503551257550.406722977634-0.0232411150581.2935561609778.0792125631-47.050446161322.8527853688
63.95458734681-1.508132091710.3372967528149.0881490501-4.418135736167.318332815661.059416186460.261568174756-1.45051963035-0.3322605781430.09624619543141.225992513261.33279532687-1.53587974544-0.7522749161681.19994279822-0.401586168507-0.1028145441190.818994790502-0.1421955165550.87248041357652.0262532428-50.4131339619.1650268654
76.81335233975-0.723198437362-1.608462375516.2308571787-0.5967869074713.318523243130.3620205176671.48307236405-0.826509401983-1.08253667458-0.531299820598-0.811873653816-0.1090364409560.2042513380770.09432370405241.2532745266-0.2113917957950.1712927201620.819446756726-0.2471974303430.73590501323966.8263963862-46.670973110212.8423726197
86.611040149461.268214958392.309621114257.065465037532.479880955528.60202909684-0.461498410584-0.189433530838-0.8160930483320.322658913340.32687045344-1.036178844020.5641367605840.504253421237-0.05302025402820.8753291831580.136554551931-0.02300595057530.562529750639-0.195629421420.70600533917168.2039904818-45.503067528424.5075190262
91.418752103220.0551665476341-1.440482997253.719751704332.173629215282.794145991710.8722222156710.830376618273-1.30048190177-0.546749325847-0.1795396350140.6021851486171.00963229260.468838416091-1.549630945091.39136120205-0.368624592166-0.02301523951190.744979086045-0.4963520543750.87362967601860.5108457198-48.028877370114.1300370494
103.11260173714-1.730134159061.110830795787.239834289353.71889078177.085541155010.5102327107122.40571770041-1.25324569182-2.24131755641-0.237742682982-0.4381028151231.08444131607-0.091699966985-0.2411149229251.478399607150.0579073974250.1126099063211.0048106423-0.3410254996580.99264301088167.4006056945-55.30803399810.7578224447
113.846811546020.235255461751-0.6723138238272.866386545430.008604061857820.375158578570.0114139653386-0.37928318391-0.0977434161027-0.4605631137490.3112671521210.221252182978-0.0877255714375-0.3388465849270.1146979759120.199113205259-0.2840842675670.07592484795091.05458645366-0.04062366530240.42107640064370.0557248217-8.7486132813424.1156418773
120.6667491933651.180282140890.08370809865742.015650651340.186396182312-0.00862930238845-0.521301250728-0.00593154370312-0.129695840429-0.3782242980350.591799451040.1928532690590.007772404744250.208903517377-0.2884407288510.183954954948-0.1582414988540.03399410553431.064131518870.01577688757830.47780969973366.0172322553-17.073982753823.2541804973
132.18256873776-0.9496146983860.09353753040691.98098886145-0.9457624026654.286691527520.1538851905230.170340753141-0.46453796808-0.393200822023-0.113650239554-0.4342406908460.573002774033-0.1086583819250.003444578801050.527893199164-0.184860089158-0.04253883577750.417845564284-0.06740587719650.57216733751558.8406274263-39.755634065723.201132648
143.94394916074-1.45052350765-0.5255379255814.34220939782-0.9462529538962.400607851550.201380705108-0.215797981046-0.515588773346-0.0522317399310.06318241623240.1581890356490.476765708075-0.602401707794-0.2511579934940.449812931275-0.217566622177-0.06221308480130.6058825147740.05972286474450.38370327231351.6544703658-37.049000597228.6862091345
153.40360199463-0.275546827848-0.8780965691293.08712373012-0.5123927085873.74876231649-0.17594125455-0.1089552571120.0377455846318-0.142075385289-0.1662985804520.4813046207050.169287620798-0.6551518866390.2493523845750.538439457686-0.1042086474270.1462736923570.333071526971-0.1749698757820.381266634404107.455719003-21.4804677881-5.81483480533
163.06205334783-0.2069410471631.536587520514.549037940180.949447190951.01909226264-0.1495815752580.4822350193880.181843090526-0.821294835619-0.3615466860180.149781791825-0.307807215474-0.558947673190.2491977442440.700950331854-0.17552778150.04887262218190.463617288279-0.1431774930570.3033514995105.72468562-23.4134166757-17.4593539189
173.470169428670.128536394806-0.4848252840541.64396079262-0.8439531207023.26663434116-0.321786464984-0.483141277255-0.4147224495360.231699934651-0.1735197350430.2378647178861.42807209429-0.43648356840.4321675151250.831233862694-0.1128978741660.1940421516140.363105402065-0.01568649645450.455777709777106.947580409-32.6484916681-4.3893650073
183.14949411548-1.342510098860.4706269567982.639791571430.3402596301491.6592748359-0.0852708069108-0.7671542185660.2292680874660.509584864072-0.0914465910207-0.1620330045610.02566397792-0.1969300705030.09295810588390.646575183947-0.1376419179380.1089150806590.441963279592-0.1402665696630.390540646904117.307327561-24.24465942743.9565110381
197.94368089726-1.61436233884-3.26699901266.31537330944-1.789216936364.792759338490.139018876793-1.37797952332-0.338264027810.3856605976540.178614012189-0.3479009724130.3795945823820.671670585535-0.3415558209670.704657701803-0.155106451877-0.007427843303290.4393612373220.004803747747640.383965715417121.655214333-33.71383402474.80993675623
202.46801898941.825278772681.047902994422.48009045531-1.574641050665.344314542030.253770552370.1201126697620.145071632903-1.127794059730.345148902643-0.9660524109620.7936369757460.1240039464690.3625862034090.653788095628-0.07707325658740.2352656787220.295946851513-0.09876367276920.447239644655122.596240309-23.1843442361-17.186736315
211.57471392-1.32835463339-0.2195305234563.24160010640.8214963021443.747770824930.07479854452530.06345941808170.780886462937-0.481927597263-0.353887003550.290620166727-0.631589142148-0.2891149927770.2502085210750.560179749378-0.07765201030290.09955061928370.367739623861-0.09832520658281.04767297392113.9248342866.13421067927-11.2727244947
222.566097445861.674311090651.172928674289.187183487832.90210047594.358091260210.0333843046623-0.7293084368820.6034207197840.262594684244-0.2586200129440.231165059535-0.224353879156-0.3043760963170.2377071038720.560348540913-0.0590782014163-0.009637407216720.232369797175-0.1189454074980.87063370487115.9377136397.71738548423-4.9227841822
231.020223806211.589311894870.8414328431353.691586904071.586163296722.961068536860.11368108636-0.271469339180.9631566681710.36353149128-0.5510160430580.367337498606-0.22026872591-0.2631282658360.373262285170.58017772474-0.08671665423980.01647338125830.380687380365-0.1078322379840.87835649358117.35684700310.3977216545-3.95037881008
242.975253255270.0696770873524-0.639258639334.74151011112-2.805768603932.07454014945-0.307868063774-0.6685870524970.5527905920940.8783917763320.063701205320.2279866740220.567781542063-0.142389927970.2167561055530.8412044518520.03448580776370.06540834563660.581559688685-0.3589559275090.582526357136102.875482984-6.627373613184.1141751064
257.18916786483-4.378554848681.866820155715.62299635407-2.311522437333.764152685990.0824343993968-0.05054050425330.9894330090360.0548434729797-0.4172635524570.364854833487-0.193842624067-0.3614211326640.2808496223040.490974292191-0.09535084711980.08072247760660.440269817851-0.255652161540.692772109198.6347965219-6.35949737186-6.13265053791
266.98810000656-1.903307629511.934045936271.30611381792-2.881851987217.64077754453-0.1662283838860.803571967951.00500497980.494953014971-0.002246770639390.0918557723031-0.655102512891-1.089812521360.001102353165240.503652180270.06070296561030.1090421958220.560298732106-0.117198914860.84021411039796.0549466445-0.863106320978-9.5329868082
272.84252043587-1.767497514993.543188703944.31086002461-3.033574951225.45938865035-0.12857970483-0.5022163818390.344206549601-0.118723836092-0.208932155092-0.1154088756280.107760470359-1.086106351940.3390916146240.6292603087840.05314500386470.2320056396440.589263004446-0.2888415903010.89025379426895.0267684488-0.06417121899320.992606822055
283.64924962879-2.782340043660.9814161108343.50437628866-2.236258457061.867972994130.148918113003-0.895293258333-0.1279067224070.2534718159870.02455739302810.4018216867570.0269570783455-0.4087724949780.005988992036580.775916450628-0.2307021067840.1230808583860.456450609275-0.03185934045730.194890328214114.684873794-33.3913990199-3.33891733173
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'D' and (resid 23 through 54 )
3X-RAY DIFFRACTION3chain 'D' and (resid 55 through 77 )
4X-RAY DIFFRACTION4chain 'D' and (resid 78 through 105 )
5X-RAY DIFFRACTION5chain 'D' and (resid 106 through 119 )
6X-RAY DIFFRACTION6chain 'D' and (resid 120 through 132 )
7X-RAY DIFFRACTION7chain 'D' and (resid 133 through 153 )
8X-RAY DIFFRACTION8chain 'D' and (resid 154 through 168 )
9X-RAY DIFFRACTION9chain 'D' and (resid 169 through 188 )
10X-RAY DIFFRACTION10chain 'D' and (resid 189 through 202 )
11X-RAY DIFFRACTION11chain 'E' and (resid 2 through 93 )
12X-RAY DIFFRACTION12chain 'E' and (resid 94 through 120 )
13X-RAY DIFFRACTION13chain 'E' and (resid 121 through 186 )
14X-RAY DIFFRACTION14chain 'E' and (resid 187 through 241 )
15X-RAY DIFFRACTION15chain 'A' and (resid 1 through 37 )
16X-RAY DIFFRACTION16chain 'A' and (resid 38 through 56 )
17X-RAY DIFFRACTION17chain 'A' and (resid 57 through 84 )
18X-RAY DIFFRACTION18chain 'A' and (resid 85 through 137 )
19X-RAY DIFFRACTION19chain 'A' and (resid 138 through 162 )
20X-RAY DIFFRACTION20chain 'A' and (resid 163 through 174 )
21X-RAY DIFFRACTION21chain 'A' and (resid 175 through 197 )
22X-RAY DIFFRACTION22chain 'A' and (resid 198 through 219 )
23X-RAY DIFFRACTION23chain 'A' and (resid 220 through 275 )
24X-RAY DIFFRACTION24chain 'B' and (resid 1 through 12 )
25X-RAY DIFFRACTION25chain 'B' and (resid 13 through 62 )
26X-RAY DIFFRACTION26chain 'B' and (resid 63 through 78 )
27X-RAY DIFFRACTION27chain 'B' and (resid 79 through 100 )
28X-RAY DIFFRACTION28chain 'C' and (resid 1 through 9 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る