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- PDB-6vm9: T4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide ... -

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基本情報

登録情報
データベース: PDB / ID: 6vm9
タイトルT4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV)
要素
  • Beta-2-microglobulin
  • MHC class I antigen, A-2 alpha chain
  • Melanocyte protein PMEL
  • T4H2 T cell receptor alpha chain
  • T4H2 T cell receptor beta chain
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 / 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 / melanosome / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / 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 / Golgi membrane / external side of plasma 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: 2.9 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9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: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanocyte protein PMEL
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)94,9655
ポリマ－94,9655
非ポリマー00
水00
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanocyte protein PMEL

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)94,9655
ポリマ－94,9655
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
単位格子
Length a, b, c (Å)129.744, 129.744, 113.440
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

#1: 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
#2: 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
#3: 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: 1035.213 Da / 分子数: 1 / Fragment: epitope (UNP residues 209-217) / Mutation: T210M / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P40967
#4: 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
#5: 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
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: 2.9 Å3/Da / 溶媒含有率: 57.62 %
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, seeded with crushed crystals

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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: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年8月16日
放射モノクロメーター: 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 Å / 相対比: 1
反射解像度: 2.9→50 Å / Num. obs: 24229 / % possible obs: 99.6 % / 冗長度: 9.6 % / Biso Wilson estimate: 88 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Χ2: 1.111 / Net I/σ(I): 24.2
反射 シェル解像度: 2.9→2.95 Å / 冗長度: 7.1 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1125 / CC1/2: 0.864 / CC star: 0.963 / Rpim(I) all: 0.324 / Rrim(I) all: 0.943 / Χ2: 0.961 / % possible all: 94.9

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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 1TVB

1tvb


解像度: 2.9→42.7 Å / SU ML: 0.4764 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 31.716
Rfactor反射数%反射
Rfree0.2501 1836 8.19 %
Rwork0.2104 --
obs0.2137 22405 92.11 %
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: 103.23 Å2
精密化ステップサイクル: LAST / 解像度: 2.9→42.7 Å
タンパク質核酸リガンド溶媒全体
原子数6642 0 0 0 6642
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00216825
X-RAY DIFFRACTIONf_angle_d0.48889271
X-RAY DIFFRACTIONf_chiral_restr0.0426964
X-RAY DIFFRACTIONf_plane_restr0.00281218
X-RAY DIFFRACTIONf_dihedral_angle_d19.53862509
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.51061020.4061186X-RAY DIFFRACTION69.28
2.97-3.060.40221200.37921300X-RAY DIFFRACTION76.8
3.06-3.160.32941280.29861423X-RAY DIFFRACTION83.3
3.16-3.270.31571420.28741541X-RAY DIFFRACTION89.47
3.27-3.40.31311350.28151577X-RAY DIFFRACTION92.19
3.4-3.550.3461420.26031605X-RAY DIFFRACTION94.48
3.55-3.740.30421540.24811674X-RAY DIFFRACTION97.03
3.74-3.980.25261540.22971661X-RAY DIFFRACTION98.21
3.98-4.280.24571540.20121698X-RAY DIFFRACTION98.88
4.28-4.710.24091520.17271700X-RAY DIFFRACTION99.36
4.71-5.390.18241520.1721734X-RAY DIFFRACTION99.42
5.39-6.790.24051510.19831723X-RAY DIFFRACTION99.68
6.79-42.70.20921500.17561747X-RAY DIFFRACTION98.91
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)
15.150661035351.233433098771.124967968072.126898155020.9011720833042.914675199950.4616415617210.513139459849-0.738107704019-0.229781329719-0.0656160676961-0.2280783227340.3792424389690.133862967948-0.2706063780851.064185050390.365132895451-0.06331952760050.624117833368-0.1074889942580.80785615119399.9260558676-7.71802376726-33.6183556195
28.630067239350.9994628977761.62078354653.9176995786-1.443761376932.628942281570.219878071207-0.911126246544-0.5838747337140.5152026540020.008061924123640.09744357334930.244350119650.130759422319-0.2756785833441.002053270360.167673830288-0.0187664536260.811730439039-0.04009689227770.72887750065997.2881627144-8.15768544102-21.9960556934
32.34214145319-0.3770683200891.250939280740.571617573529-0.7731455546216.8240728671-0.08447763913530.2074223129-0.0407084176653-0.400013610616-0.453293846810.6715771014270.194689589031-0.5710627315360.3736071585571.200441703820.409617975521-0.1468316949250.885384132079-0.2220206694630.82964895331689.8953325494-2.5587868098-35.2892754662
43.691762667530.9266587698031.528848093711.12374440856-0.5993030115951.985771462340.3976440646390.894807539984-0.283562565246-0.122385547366-0.0180204504316-0.1788037106850.4940166431450.506130225535-0.2635206282281.176690156030.406857951818-0.05993192279550.777056248869-0.07863572579380.76994699393102.5773842860.245679126234-40.9501670174
55.71854777333-0.5014844721760.2192020698945.215501103821.926527831333.24632077750.374092460281.10970912550.294302057923-1.29208372447-0.2551226090460.208370100119-0.457174894721-0.0699852882001-0.1749204229821.249736733110.3983028532790.02238547532760.8339107197040.08121848604940.73364578843199.66131336088.37487989923-45.9757807316
65.403152576580.24007691806-1.430884236280.02348381921110.3113040740674.303526399430.34718982078-0.5085034062210.5043993110280.03086222075180.2666834846110.211010373215-0.358519985310.46644148235-0.5734932887150.9095873632440.147571140205-0.0921530759480.512812728628-0.0914954633960.706401408512106.3268129526.23977620763-22.2657055646
72.95126704955-0.2926042631540.173079941772.82103784886-0.9277184341910.200446977570.007399797361270.136993214407-0.508557802692-0.032825288985-0.256913324065-0.323720680176-0.155286151130.0915034834830.1988264058521.05516979350.333555380481-0.1017930105160.796822440603-0.02315565516251.03915419464126.830432069-16.4383279078-27.9988901081
86.507853142322.611422049970.1930568359011.67583912539-1.568096520652.8276869046-0.2205935085630.508097185932-0.764709653602-0.277529428050.08868041011-0.2719739347330.3286294820980.3412116311390.1680911225741.005245324050.340076872269-0.05439246549790.782434323049-0.1163089107210.9446441884131.40161851-15.736146923-35.0128446787
95.280483623790.851903326612-1.398310712382.998774459931.71424721373.90038542429-0.2413447684810.106552090858-0.202435904682-0.120423954337-0.488811464897-0.680443079616-0.409573623626-0.3876681774720.5664632969641.049055926960.182280515475-0.02660580453560.630397599217-0.1294766100980.943854639121113.944520745-22.7767319704-34.9475189191
104.009281172640.22302892812-0.1768256070663.37361757419-0.1261394182684.20952390192-0.00801930840832-0.233956279973-0.5169710031880.200411812682-0.2940912416450.380686694644-0.335183209462-0.6641827954790.2958902595790.987423571880.232185251108-0.01208785874940.698938413303-0.1773662186870.932246416734105.811128937-24.3976774906-33.7222646908
114.229817784710.6448276245051.977667932993.14130808976-0.7883558048136.26617892250.2214882110420.00847146498035-0.463900323202-0.54737946208-0.383719222769-0.1833602904940.384281168671-0.3239387419650.2040903338690.9668339709850.2417474934520.02256752421110.599457151637-0.1024825108750.840281125669110.371818964-24.8606227684-33.6744192983
125.05107966772-0.06655885901142.078048476062.762532310750.2654782354255.49017860474-0.1324075760210.258831885517-0.73220649228-0.1936195061470.433086987238-0.108280343599-0.06216369011580.431007370231-0.2918779966961.33466247520.3502634087640.05564464053160.707899534541-0.1015728293630.981281430397112.997116365-29.0843984283-40.8519734202
132.555656430510.50363740339-0.9012135203954.917800598321.830689069911.1895906075-1.830512534880.08951789106880.358389450905-0.53170964315-0.1612380973730.796989600618-1.5423468379-0.4245695898431.993179455871.198496908530.264559525616-0.2157971434780.966820383165-0.0961950296040.78481233461593.54429916414.428442803-36.044092086
143.70484488432.298333920760.5483370739412.072015175550.549157022934.940976590970.30025041033-0.650661200211-0.8503693937281.58291507958-0.0248942702823-0.8350749835840.275853437335-0.437880356747-0.1823621510221.05101312930.100384622622-0.07383039788080.7899884289440.2227598965451.0662483571943.083836603-30.570215401-19.9681216376
156.035814653783.110111720970.9929678557485.08221826039-1.493890776884.07915856330.03545524458410.0549845829575-0.4570922643090.05543799008590.01738140526140.1739462874240.0587262956788-0.207717345508-0.04148902888580.7705871597650.1961042738350.04431483954670.555830732290.04429473297460.62086849644740.9080615744-23.9181403457-28.1369305
160.912032701323-0.334305552040.4903551664980.0278336747025-0.1207738940122.30963035698-0.10321612361-0.227995533778-0.8123980849050.863513270312-0.392756622785-0.09690899463890.850939874104-0.2767907785380.3289373298611.236753663720.07883980053740.1021818213750.8099481032230.156505378531.4144073789151.7543418831-44.221123487-22.6849251234
173.825918881191.55261282427-0.08988966701355.013049783580.8474241508737.794302216850.0161617353651-0.179178688412-0.5812881381460.991212029660.186399344746-0.2459602558750.6423824729921.53965736122-0.3023733820531.319866423380.3322642103820.01832849464521.387117620670.1629911594361.1256496412269.4750852241-47.705178522-16.00658104
184.785087840271.46727705476-0.286596226246.412701982210.1839662772665.95742249528-0.707605874793-0.00708925721796-0.277212176594-0.1458105721770.2730133664780.2422317960951.220682892120.4522472525760.6088708810651.410257138650.155188489589-0.02536851990960.8195757084230.1788546936821.1905667646962.1034962904-45.6117130637-25.2078605629
193.330227845721.312619151130.909125589954.856631426290.07693082506474.770974794760.214658978948-1.81432832511-0.8198233787490.9632104401130.0452046551221-0.09813742167030.851402366285-0.871636741655-0.1327874482081.779831070440.243774110143-0.01667021929631.593634512620.3442181873891.2591730704967.0183036386-50.7762893435-13.2364378317
205.663989434070.8142581707584.376314905524.14517171712-0.8506499187326.20187350150.4677203441610.1390129269350.478547800771-0.569229143333-0.204651890763-0.492995214885-0.1925616795330.261213777748-0.2736542357720.8584876558140.2009612422830.2724594291810.7650747879390.005973911028910.89396942744759.2242508039-8.88969780237-25.9487735488
213.33888115731-2.36827052642-0.03769578214632.621706625430.6202007825513.02531437706-0.295777309092-0.769362161748-0.1008599507290.1379457414860.508007751106-0.0234233564442-0.3056972131920.330895698241-0.1083230470150.791955147250.2194546006050.1665934227630.8065224103450.0009797627991280.80605767390163.4748361347-17.0775724862-24.6574878773
222.263427095163.057208454070.7597060236544.539866808441.834762865973.28650842474-0.0704691884314-0.344439913686-0.3282565747560.3586819887030.295059361485-0.2688539709770.41768696660.341524575052-0.1652169088360.8693407893620.341978144442-0.07646526967880.998239828398-0.01618834739250.88606217663174.6700399117-38.2377163473-26.6643616419
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 275 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 20 )
10X-RAY DIFFRACTION10chain 'B' and (resid 21 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 84 )
12X-RAY DIFFRACTION12chain 'B' and (resid 85 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 9 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 24 )
15X-RAY DIFFRACTION15chain 'D' and (resid 25 through 102 )
16X-RAY DIFFRACTION16chain 'D' and (resid 103 through 119 )
17X-RAY DIFFRACTION17chain 'D' and (resid 120 through 153 )
18X-RAY DIFFRACTION18chain 'D' and (resid 154 through 168 )
19X-RAY DIFFRACTION19chain 'D' and (resid 169 through 202 )
20X-RAY DIFFRACTION20chain 'E' and (resid 2 through 93 )
21X-RAY DIFFRACTION21chain 'E' and (resid 94 through 120 )
22X-RAY DIFFRACTION22chain 'E' and (resid 121 through 241 )

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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