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- PDB-6pvd: Structure of human MAIT A-F7 TCR in complex with human MR1-NV18.1 -

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基本情報

登録情報
データベース: PDB / ID: 6pvd
タイトルStructure of human MAIT A-F7 TCR in complex with human MR1-NV18.1
要素
  • Beta-2-microglobulin
  • Human TCR alpha chain
  • Human TCR beta chain
  • Major histocompatibility complex class I-related gene protein
キーワードIMMUNE SYSTEM / MAIT / MR1
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 / phagocytic vesicle membrane / recycling endosome 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 / iron ion transport / negative regulation of neuron projection development / 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 / 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
ACETATE ION / Chem-N18 / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.14 Å
データ登録者Awad, W. / 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: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: Ligand-dependent downregulation of MR1 cell surface expression.
著者: Salio, M. / Awad, W. / Veerapen, N. / Gonzalez-Lopez, C. / Kulicke, C. / Waithe, D. / Martens, A.W.J. / Lewinsohn, D.M. / Hobrath, J.V. / Cox, L.R. / Rossjohn, J. / Besra, G.S. / Cerundolo, V.
履歴
登録2019年7月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年4月1日Provider: repository / タイプ: Initial release
改定 1.12020年5月6日Group: Database references / カテゴリ: citation / Item: _citation.title
改定 1.22020年5月13日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.32020年5月27日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.42023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 1.52024年11月6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: Human TCR alpha chain
E: Human TCR beta chain
F: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,84914
ポリマ－188,1008
非ポリマー7496
水21,0421168
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,5348
ポリマ－94,0504
非ポリマー4844
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: Human TCR alpha chain
E: Human 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)94,3146
ポリマ－94,0504
非ポリマー2642
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)216.057, 70.112, 142.874
Angle α, β, γ (deg.)90.000, 103.970, 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 Human 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 Human 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 , 5種, 1174分子

#5: 化合物 ChemComp-N18 / methyl N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alaninate


分子量: 241.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C9H11N3O5 / タイプ: SUBJECT OF INVESTIGATION
#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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#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: 1 / 由来タイプ: 天然 / 式: Na
#8: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H3O2
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1168 / 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: 2.85 Å3/Da / 溶媒含有率: 56.79 %
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: BTP (pH 6.0 - 6.5), PEG3350 and 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: 0.9536 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年3月24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: 0.9536 Å / 相対比: 1
反射解像度: 2.14→53.49 Å / Num. obs: 113315 / % possible obs: 98.7 % / 冗長度: 4.9 % / Biso Wilson estimate: 42.56 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.15
反射 シェル解像度: 2.14→2.216 Å / Num. unique obs: 11169 / CC1/2: 0.799

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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
PHENIX1.16_3549精密化
XDSデータ削減
Aimless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: 2.14→53.49 Å / SU ML: 0.2255 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 22.1671
Rfactor反射数%反射
Rfree0.1977 5592 4.94 %
Rwork0.1683 --
obs0.1697 113270 98.71 %
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: 49.42 Å2
精密化ステップサイクル: LAST / 解像度: 2.14→53.49 Å
タンパク質核酸リガンド溶媒全体
原子数12705 0 51 1168 13924
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003113494
X-RAY DIFFRACTIONf_angle_d0.616518441
X-RAY DIFFRACTIONf_chiral_restr0.04461969
X-RAY DIFFRACTIONf_plane_restr0.00372413
X-RAY DIFFRACTIONf_dihedral_angle_d16.45378151
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.160.2641820.23723515X-RAY DIFFRACTION98.19
2.16-2.190.23151860.23053574X-RAY DIFFRACTION98.2
2.19-2.220.24791940.22263517X-RAY DIFFRACTION98.12
2.22-2.240.29531760.22713544X-RAY DIFFRACTION98.18
2.24-2.270.28361940.22483594X-RAY DIFFRACTION98.26
2.27-2.310.26871780.22873494X-RAY DIFFRACTION98.23
2.31-2.340.28222080.21983550X-RAY DIFFRACTION98.33
2.34-2.370.22711920.21473539X-RAY DIFFRACTION98.39
2.37-2.410.27981820.20863605X-RAY DIFFRACTION98.41
2.41-2.450.25361820.2133532X-RAY DIFFRACTION98.54
2.45-2.490.2541800.20993567X-RAY DIFFRACTION98.53
2.49-2.540.26351800.20873577X-RAY DIFFRACTION98.56
2.54-2.590.26391680.20223609X-RAY DIFFRACTION98.67
2.59-2.640.27081720.20883559X-RAY DIFFRACTION98.65
2.64-2.70.26671870.20183605X-RAY DIFFRACTION98.62
2.7-2.760.23351810.19843528X-RAY DIFFRACTION98.85
2.76-2.830.22361870.19983620X-RAY DIFFRACTION98.88
2.83-2.90.23122030.18593583X-RAY DIFFRACTION98.88
2.9-2.990.20751960.18863572X-RAY DIFFRACTION98.92
2.99-3.090.22591930.1773589X-RAY DIFFRACTION99.08
3.09-3.20.19751780.17593607X-RAY DIFFRACTION99.08
3.2-3.320.20861930.17163616X-RAY DIFFRACTION99.06
3.32-3.480.18391770.15743598X-RAY DIFFRACTION99.03
3.48-3.660.16561910.14883619X-RAY DIFFRACTION98.83
3.66-3.890.16811980.14663601X-RAY DIFFRACTION98.86
3.89-4.190.18491660.13953644X-RAY DIFFRACTION99.14
4.19-4.610.14011980.1173628X-RAY DIFFRACTION99.38
4.61-5.280.13691840.12593648X-RAY DIFFRACTION99.25
5.28-6.650.17881980.16513667X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92166706286-0.7114206020280.355771247872.165070360960.4565773677741.832990755250.0462993855630.2695773714020.203724704823-0.4010219736850.00250993013557-0.2337387733410.1168033510350.170718962237-0.04742279623790.276529154753-0.06698271752970.05364794165040.3526032731550.01240851062280.2897435343851.45282206977.456660549224.067286732
21.47923368247-0.649312676045-0.03272505500042.334354895560.2503157733020.8109262422490.0309093504506-0.07635043973220.1124929889220.0668763145922-0.02924738624790.285682954395-0.0149635833404-0.06795605581060.01183927603910.231890161415-0.0160500360318-0.003432632046880.294917535567-0.008035385304260.29651757276939.409907736980.6677665815234.767976772
31.960602942390.3566698312541.097857565581.14448247938-0.06176368254771.337700456380.05415121725980.0120425751929-0.07807776436590.1425975104880.126270991998-0.3608777307640.1052717968110.207104432165-0.1175413540280.2695782340080.0802072822201-0.04122637830330.405397419244-0.1082175863950.39856400561664.336140801670.197216694243.410734626
41.137063619620.669236053199-0.2470027462820.876494253287-0.1503309676221.451123521190.0220423084859-0.2465724538050.4508709847020.309444885930.050609445865-0.114493186752-0.37264497073-0.115918548047-0.08702752737640.409248249520.135733260673-0.1006742738880.600119706912-0.2142216193710.5798899593968.776568439179.5672952361256.87627829
52.46752225718-0.447733830730.7082502261082.64149628013-0.5730564259311.982841392320.2040166638290.2756612576260.6883591791030.1311113434470.39108097082-0.192671087173-0.4220399087420.201207975917-0.6047315766750.468336702595-0.02081197591470.02040807916250.357352101496-0.0538137903010.72841261564454.875918592696.8444288735235.827409578
60.789020554383-0.6351070968971.010425615092.45645839752-0.9632020321281.2740495475-0.02720520930350.0898372270480.02671172239040.356341795273-0.0638504974964-0.087147226408-0.1092993605420.1973958812450.04325258414190.386828367916-0.0459968571845-0.08695822220.566370347866-0.1132425356920.74479902410771.06598480987.8812434016240.623442176
71.22400782999-0.1096714680540.239383250202-0.00089268446576-0.05566609740321.34349493294-0.33477283758-0.12532638682-0.1734049067870.160257097583-0.0850527551815-0.7061566015790.01995568972620.8728085159240.2755460622110.3324326807570.0289842089333-0.1356739303410.953662885788-0.03511007427320.96956643855883.980963884379.444681254241.411587304
82.214672760.191702588428-0.1359905053560.1589276606630.1951020589151.28421449420.09682173927810.2719078199210.255569686221-0.2881130953820.0844680788283-0.306641247404-0.03627861300380.354697778313-0.1372976441950.371708538838-0.142454087485-0.02481859912020.6367872338930.02730835741310.73083866764769.608557057988.8616158733232.813948479
92.648430034921.734079385720.06293407098941.205242404710.03036459197450.0840268006016-0.1862985261320.335426051570.0835071106208-0.294476992956-0.148898294765-0.4139596170880.1670731380910.1987961916940.1525592608770.516484119457-0.3439247180910.03574095594751.180298107240.05674821804261.0570405236977.793730336388.9379074017227.128597818
107.74405887601-0.757707440799-2.28510434771.54893281533-0.2140480956382.155842182590.424045184270.1912189643870.1918444062380.1326221650150.00902226333078-0.379046953509-0.03873795910480.270264682431-0.3536297432260.296208021987-0.039399164469-0.01806060715860.357823593396-0.02924374030380.40284106925156.423028978883.7573050598233.428736302
114.328987757340.0745894195384-0.3224510526540.46164489994-0.08096817595950.808352269110.002317079255350.415600452925-0.153062284413-0.1925995878820.0767896485016-0.2347074300110.1112970144410.406727214279-0.05785825297540.284541580777-0.04448419875570.04858353283970.605807181473-0.03749092778660.57777960554972.164497778583.7508349152232.484217132
120.753861235942-0.5254244909480.3813192807360.366049518317-0.2656908873520.176431351381-0.05671417928190.00714093648987-0.063053344857-0.00132554720391-0.0119435871825-0.207321063962-0.05266596935390.2033778674780.07063182130740.474566319229-0.113371463547-0.1313813371961.416779225960.01529504296381.1970253486788.712657099989.7451491244238.522119461
132.942931772670.818462825538-0.525030555730.4575230806630.389229745551.310612846560.4927130883340.1094026430510.256620977803-0.08416395767780.0537815893038-0.277189203099-0.1640072657370.253663673267-0.4713789735120.471111760617-0.159416939472-0.03797088304770.7086652083420.08343588856851.2484478458574.242956356294.4429478251232.939562677
140.6110644883320.8465035918390.02216304678211.15977757607-0.02809282620210.2844568153110.219805499125-0.002320969774330.563604056865-0.0342182973869-0.00656103696891-0.697718858388-0.5723548616270.427709404969-0.2481181332950.544407766447-0.194313865873-0.008109052256820.6913105010290.09002104015120.97657123610263.4535883599101.049675762232.312621362
153.352666456140.65301357732-1.120828984752.019369903691.055696960873.02912401779-0.154157753557-0.09696727491720.003170583945970.5985244586190.501801804284-0.1117751112960.09955775902090.694720394931-0.370587390160.601800673738-0.126754895939-0.1895145988030.812717170774-0.1275862359450.92280395341677.3160099293.0267397997240.815468111
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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 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 19 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 97 )
16X-RAY DIFFRACTION16chain 'C' and (resid 0 through 84 )
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 237 )
19X-RAY DIFFRACTION19chain 'C' and (resid 238 through 270 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 17 )
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 37 )
22X-RAY DIFFRACTION22chain 'D' and (resid 38 through 52 )
23X-RAY DIFFRACTION23chain 'D' and (resid 53 through 75 )
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 102 )
25X-RAY DIFFRACTION25chain 'D' and (resid 103 through 116 )
26X-RAY DIFFRACTION26chain 'D' and (resid 117 through 150 )
27X-RAY DIFFRACTION27chain 'D' and (resid 151 through 175 )
28X-RAY DIFFRACTION28chain 'D' and (resid 176 through 198 )
29X-RAY DIFFRACTION29chain 'E' and (resid 3 through 37 )
30X-RAY DIFFRACTION30chain 'E' and (resid 38 through 63 )
31X-RAY DIFFRACTION31chain 'E' and (resid 64 through 94 )
32X-RAY DIFFRACTION32chain 'E' and (resid 95 through 109 )
33X-RAY DIFFRACTION33chain 'E' and (resid 110 through 124 )
34X-RAY DIFFRACTION34chain 'E' and (resid 125 through 162 )
35X-RAY DIFFRACTION35chain 'E' and (resid 163 through 188 )
36X-RAY DIFFRACTION36chain 'E' and (resid 189 through 203 )
37X-RAY DIFFRACTION37chain 'E' and (resid 204 through 225 )
38X-RAY DIFFRACTION38chain 'E' and (resid 226 through 243 )
39X-RAY DIFFRACTION39chain 'F' and (resid 0 through 11 )
40X-RAY DIFFRACTION40chain 'F' and (resid 12 through 19 )
41X-RAY DIFFRACTION41chain 'F' and (resid 20 through 41 )
42X-RAY DIFFRACTION42chain 'F' and (resid 42 through 61 )
43X-RAY DIFFRACTION43chain 'F' and (resid 62 through 71 )
44X-RAY DIFFRACTION44chain 'F' and (resid 72 through 99 )
45X-RAY DIFFRACTION45chain 'G' and (resid 2 through 52 )
46X-RAY DIFFRACTION46chain 'G' and (resid 53 through 120 )
47X-RAY DIFFRACTION47chain 'G' and (resid 121 through 201 )
48X-RAY DIFFRACTION48chain 'H' and (resid 1 through 94 )
49X-RAY DIFFRACTION49chain 'H' and (resid 95 through 109 )
50X-RAY DIFFRACTION50chain 'H' and (resid 110 through 124 )
51X-RAY DIFFRACTION51chain 'H' and (resid 125 through 162 )
52X-RAY DIFFRACTION52chain 'H' and (resid 163 through 202 )
53X-RAY DIFFRACTION53chain 'H' and (resid 203 through 215 )
54X-RAY DIFFRACTION54chain '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

他の情報も見る