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- PDB-7n6e: TCR peptide HLA-A2 complex -

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基本情報

登録情報
データベース: PDB / ID: 7n6e
タイトルTCR peptide HLA-A2 complex
要素
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S1
  • TRAV12-1 TCR-alpha
  • TRBV19 TCR beta
キーワードIMMUNE SYSTEM/VIRAL PROTEIN / T cell receptor / Human Leucocyte Antigen / SARS-CoV-2 / IMMUNE SYSTEM-VIRAL PROTEIN complex
機能・相同性
機能・相同性情報


antigen processing and presentation of peptide antigen via MHC class I / : / : / 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 ...antigen processing and presentation of peptide antigen via MHC class I / : / : / 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 / 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / amyloid fibril formation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
類似検索 - 分子機能
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 / : ...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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / 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
Spike glycoprotein / Beta-2-microglobulin / MHC class I antigen
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Chaurasia, P. / Rossjohn, J. / Petersen, J.
引用ジャーナル: J.Biol.Chem. / 年: 2021
タイトル: Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.
著者: Chaurasia, P. / Nguyen, T.H.O. / Rowntree, L.C. / Juno, J.A. / Wheatley, A.K. / Kent, S.J. / Kedzierska, K. / Rossjohn, J. / Petersen, J.
履歴
登録2021年6月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年7月28日Provider: repository / タイプ: Initial release
改定 1.12021年8月25日Group: Database references / Refinement description
カテゴリ: citation / citation_author ...citation / citation_author / database_2 / refine_hist
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high
改定 1.22021年9月22日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.32023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年11月13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

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集合体

登録構造単位
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
D: MHC class I antigen
E: Beta-2-microglobulin
F: Spike protein S1
G: TRAV12-1 TCR-alpha
I: TRAV12-1 TCR-alpha
H: TRBV19 TCR beta
J: TRBV19 TCR beta


分子量 (理論値)分子数
合計 (水以外)190,55310
ポリマ－190,55310
非ポリマー00
水00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
I: TRAV12-1 TCR-alpha
J: TRBV19 TCR beta


分子量 (理論値)分子数
合計 (水以外)95,2775
ポリマ－95,2775
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: Spike protein S1
G: TRAV12-1 TCR-alpha
H: TRBV19 TCR beta


分子量 (理論値)分子数
合計 (水以外)95,2775
ポリマ－95,2775
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)63.832, 95.131, 168.755
Angle α, β, γ (deg.)90.000, 100.182, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 20 or resid 23...
d_2ens_1(chain "D" and (resid 1 through 16 or (resid 17...
d_1ens_2(chain "B" and (resid 1 through 37 or (resid 38...
d_2ens_2(chain "E" and (resid 1 through 57 or (resid 58...
d_1ens_3chain "C"
d_2ens_3chain "F"
d_1ens_4(chain "G" and (resid 1 through 2 or resid 4...
d_2ens_4(chain "I" and ((resid 1 through 2 and (name N...
d_1ens_5(chain "H" and (resid 3 through 13 or (resid 14...
d_2ens_5(chain "J" and (resid 3 through 14 or resid 16...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYPROA1 - 20
d_12ens_1ILEGLYA23 - 175
d_13ens_1GLUGLUA177 - 251
d_14ens_1ARGTRPA253 - 271
d_21ens_1GLYPROD1 - 20
d_22ens_1ILEGLYD23 - 175
d_23ens_1GLUGLUD177 - 222
d_24ens_1GLNGLUD226 - 254
d_25ens_1ARGTRPD256 - 274
d_11ens_2ILETHRB1 - 68
d_12ens_2PHEMETB70 - 99
d_21ens_2ILETHRE1 - 68
d_22ens_2PHEMETE70 - 99
d_11ens_3TYRLEUC1 - 9
d_21ens_3TYRLEUF1 - 9
d_11ens_4ARGLYSG1 - 2
d_12ens_4VALASNG4 - 91
d_13ens_4ASNLEUG93 - 120
d_14ens_4ASPSERG122 - 138
d_15ens_4THRASNG140 - 175
d_16ens_4SERALAG177 - 180
d_17ens_4ALASERG182 - 198
d_21ens_4ARGLYSH1 - 2
d_22ens_4VALASNH4 - 91
d_23ens_4ASNLEUH93 - 120
d_24ens_4ASPSERH122 - 138
d_25ens_4THRASNH140 - 175
d_26ens_4SERALAH177 - 180
d_27ens_4ALASERH182 - 198
d_11ens_5GLYLYSI1 - 12
d_12ens_5GLYALAI14 - 59
d_13ens_5GLYLEUI61 - 110
d_14ens_5ASPSERI112 - 127
d_15ens_5ALAALAI129 - 239
d_21ens_5GLYLYSJ1 - 12
d_22ens_5GLYALAJ14 - 59
d_23ens_5GLYLEUJ61 - 110
d_24ens_5ASPSERJ112 - 127
d_25ens_5ALAALAJ129 - 239

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

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要素

#1: タンパク質 MHC class I antigen / HLA-A*02:01


分子量: 32125.473 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: HLA-A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q861F7
#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・ペプチド Spike protein S1


分子量: 1151.377 Da / 分子数: 2 / Fragment: epitope YLQPRTFLL (UNP residues 269-277) / 由来タイプ: 合成
由来: (合成) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
参照: UniProt: P0DTC2
#4: タンパク質 TRAV12-1 TCR-alpha


分子量: 22680.018 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)
#5: タンパク質 TRBV19 TCR beta


分子量: 27440.434 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)
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: 2.65 Å3/Da / 溶媒含有率: 53.52 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: 20% PEG3350, 0.2 M sodium thiocyanate, 100 mM Tris-Cl

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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: 2021年4月10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: 3.2→47.85 Å / Num. obs: 31387 / % possible obs: 95.4 % / 冗長度: 2.5 % / Biso Wilson estimate: 53.86 Å2 / CC1/2: 0.842 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.168 / Rrim(I) all: 0.259 / Net I/σ(I): 4.16
反射 シェル解像度: 3.2→3.37 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3149 / CC1/2: 0.381 / Rpim(I) all: 0.628 / Rrim(I) all: 0.889 / % possible all: 96.17

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
PDB_EXTRACT3.27データ抽出
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: PDB entries 6VRM & 3GSO

6vrm

3gso


解像度: 3.2→47.85 Å / SU ML: 0.4991 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 30.0272
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2941 1994 6.36 %
Rwork0.2389 29365 -
obs0.2424 31359 94.92 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 56.92 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→47.85 Å
タンパク質核酸リガンド溶媒全体
原子数12993 0 0 0 12993
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001713336
X-RAY DIFFRACTIONf_angle_d0.480418135
X-RAY DIFFRACTIONf_chiral_restr0.03931917
X-RAY DIFFRACTIONf_plane_restr0.00342385
X-RAY DIFFRACTIONf_dihedral_angle_d12.35154779
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.839363330303
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.62747239221
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.256578909776
ens_4d_2GX-RAY DIFFRACTIONTorsion NCS0.898639464388
ens_5d_2IX-RAY DIFFRACTIONTorsion NCS0.760528897261
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.38191450.31812110X-RAY DIFFRACTION96.29
3.28-3.370.35291410.30072126X-RAY DIFFRACTION95.53
3.37-3.470.35481460.30352100X-RAY DIFFRACTION96.6
3.47-3.580.34811500.27562098X-RAY DIFFRACTION95.78
3.58-3.710.3061370.26492104X-RAY DIFFRACTION96.14
3.71-3.860.30751420.252108X-RAY DIFFRACTION95.91
3.86-4.030.32931490.2462094X-RAY DIFFRACTION95.37
4.03-4.240.27081440.22952109X-RAY DIFFRACTION94.82
4.24-4.510.27151380.20522068X-RAY DIFFRACTION95.05
4.51-4.860.26891380.19632096X-RAY DIFFRACTION94.42
4.86-5.340.27381410.21252089X-RAY DIFFRACTION94.25
5.35-6.120.24331430.22652074X-RAY DIFFRACTION93.9
6.12-7.70.29951390.24252095X-RAY DIFFRACTION93.43
7.7-47.850.24591410.20722094X-RAY DIFFRACTION91.71
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)
13.470714500970.1161411482411.471941017482.253192787631.433493814232.910375062580.0565146635003-0.4008224497090.0460961087618-0.1571952076960.343689887088-0.04556237895620.01150056541610.523954977429-0.05073736576470.350338942531-0.1292618545560.1332648923150.41438592368-0.08597175224280.414743527108-4.99531675953-21.993777541853.2513847242
24.086104865240.9565841662742.434007210942.310338535591.149669535313.02500977830.758281483751-0.401061523474-0.826505164050.688249856803-0.221115740325-0.2271034534651.28927419462-0.133355066732-0.8535888139510.635352818881-0.0256500261893-0.2468232867080.4623269969860.1280278690080.84755598251919.9551292955-30.408979350976.1704637131
34.38115225245-0.127174766270.13014639313.01367372654-0.7627658710593.360941691010.001324168093750.0610360563633-0.00158231584682-0.143695640248-0.502707790852-1.094267966070.390519594130.632105350703-0.08963681446320.302705512442-0.173636978624-0.05525244292510.6685194602280.13818831630.6519448800818.8194934292-16.516059100568.4803161241
44.10081502929-0.792041923220.6228992167351.16219983785-0.6801367996531.233714979080.2153413824350.4673131671190.998723810073-0.156248947256-0.47465114207-1.17504257017-0.01680446586470.524754969910.2144948394270.3281701720880.07789925220810.02947832781550.3745653784320.2222955207121.0924158266216.2548149763-10.496121287964.5676507295
51.88742530081-0.311670282208-1.202776953861.82298078641-0.2506843389651.32084746728-0.1000887583240.6867126201390.916123523629-0.467881157373-0.344243502079-1.25297370969-0.2842260045020.5062660672520.3187695464030.9541966852120.2534312676120.3479823116070.5900534415360.4419672903311.4676698921419.696461917-7.8906866278457.5813378543
62.72160131931-1.096095461140.7729125462012.065756493710.7571845172122.647432518710.05660412319760.5343192606250.346491145778-0.143226617848-0.315896394969-0.330398941801-0.08935444047990.2992626211020.1283787284880.1918247595780.03217262247070.09246409179360.715446162920.1537564246980.6200208409811.548412569-15.988091970261.7918958084
74.46512668136-0.2995574289561.031034543150.2546085871240.1875628593792.98034752154-0.123057171528-0.09532564798421.39091713412-0.386058493967-0.233717302987-1.445410259530.03825789291060.3956196869470.2391813598570.5205638885030.0800705151246-0.09255436001940.4605608255610.01441852010221.2117049625121.4378957523-8.4837177151171.277578334
81.41418001235-0.413781238673-1.053711517420.9697491111140.2174341221442.020620941110.09502332161880.02329920607980.14621780836-0.100995946076-0.0167767649124-0.0862493664753-0.09752610021440.2834566655890.2918198235460.118248476634-0.02454308469980.07767458058070.4109879625090.2800520200840.272545443979-10.6367090773-23.223029987148.0635192088
93.34226235707-0.0603794879803-1.10150182261.97115105776-1.124657247611.956941618180.122612736720.0171976041403-0.6550279726510.2705380235960.210188028310.1756996597540.578288754346-0.5752064298730.02777836854070.435719905879-0.0971038811476-0.2834951891790.5190227695350.2296129515690.5776625433780.85710930669218.158461950651.7060977047
102.035302975180.508701990516-1.713434895580.5130580312-0.211399576861.573750376720.06792259485050.6621097991670.249694513006-0.3256399590710.1341508130820.3391165593570.048629058084-0.5175788610810.2849836827120.788869233419-0.111787578629-0.5045320357340.546548391360.1959258264471.11626149877-5.1165429844120.278160011341.7612007028
113.435766853690.343967969301-0.5438980241821.12871819514-1.173022755391.87107548182-0.0767213190935-0.490064603227-0.0967590756342-0.01536221997650.1756689285860.1533612780240.0321071288731-0.4746269887620.1438769231130.405493322992-0.108461564334-0.242189848660.373132381691-0.004766756430380.4669116549339.262783383719.809503167151.9643211693
123.70178199792.01910775575-0.5834453026523.20100537041-1.070923473082.096555963480.125015771138-0.7900640071620.1550308399390.533691406729-0.4953764135320.108014759379-0.583738565997-0.2069202641740.05749210596070.278003760799-0.169264140883-0.09806777337610.470187269064-0.08159701143180.2485332916115.682405307623.817005134363.0227324782
133.615853973240.759164843026-0.07339206859591.38736236665-0.2981724699271.175993551580.15423914028-0.1170982243370.4828981820080.0771879498762-0.1615857558560.051237582863-0.3113315559870.0256650959309-0.03048943022460.577715999981-0.11389608561-0.2139009639770.183341338932-0.068218819720.43620235846913.006284906829.777969273152.101276704
143.497493613010.685732363673-1.123146687221.05347829655-0.9183472700673.087991161480.782131641046-0.6341349701510.8294692247980.3003201216690.0922620888594-0.212508665226-0.742061253004-0.00476778338291-0.1595604627650.7190784299950.2421464335880.04409272894450.645010603669-0.466120590860.878563859465-17.347327386230.466842235774.4649826988
155.219926745580.22706410076-2.926972895661.64814688457-0.4810205566066.636969375090.247181119584-0.4461721980050.441461712716-0.0828236778660.2133662885520.348695382066-0.190986924017-0.286451532428-0.1377376458880.5193925321680.185823074305-0.2850684337330.546829823592-0.2242718729930.803128876945-16.236816403925.244490844771.3239733748
164.568877859690.894392769827-1.522785251651.96310549729-0.788724473581.437392017970.784453676135-0.93084253791.28010653839-0.01791081018210.2172159919340.225466466016-1.405942800690.229865791887-0.8095372042971.214558173440.1732450711110.1094047575990.81622575115-0.4343250088281.04043921553-19.691231331437.047473066579.4996278488
172.85806198363-3.76793909255-0.4372961170795.18093557460.05960201006771.38900766162-0.05382628776-0.219978720671-0.3875788606380.188644896244-0.0332445033790.3884310452670.01257900939930.2398085279790.06482829190080.124205702787-0.1726009328750.05965414527420.6435571339880.04133068043410.298531709459-3.5524748607212.570483747270.5277940088
183.797340525290.05381699403250.226061275220.0263623919187-0.2003926125671.87845031310.02674988287990.708987505227-0.866668205894-0.304614845012-0.5726703569781.16471719569-0.238881003843-0.61000701372-0.1357105438390.4542090504330.178685789476-0.1603260850930.526680258811-0.2836323286061.15762236789-18.074223573512.77103140563.1954356517
194.74466742918-1.74906307854-0.179305684670.939688823674-0.564314743631.705421059110.009417841168810.670896560795-0.3141054233-0.221847596321-0.3065108092910.696652369972-0.199086727093-0.5309245306860.04437029962690.4064647362090.338498134542-0.1580993402780.726605862062-0.1787755496870.478706008343-9.0534270987416.490125619860.9908313862
209.446828132492.727249830121.125317816893.94242636801-2.73079518775.871903081910.13646845744-0.368960135852-1.15793536356-0.2578121001660.1644920465531.0658129-0.0366978535845-1.27745715128-0.3104648730040.725187032020.25916353488-0.4626430056461.38630345425-0.09685248390682.07532485847-32.189531811410.653373950569.5933681461
212.43298442731-0.737652501780.897321576290.268178471917-0.620499696193.110416085880.117076061791-0.229662471703-1.30416756631-0.244308022757-0.06161086124291.093192248150.087473977142-0.3667029700710.02712199716570.322896787350.0817644471447-0.123084887590.478081487709-0.08740213724831.12197905731-11.28344451274.8877586171469.3503397914
224.87591930682-0.7938511911082.045296652450.5815639573060.06282649931822.9228148714-0.0073976436918-0.714519881199-0.403006798319-0.06684418098820.2711425042781.20991647857-0.481801847648-0.604149990125-0.03487117250490.7160503657680.1276199169540.2038757388450.6126162103860.3910015496161.26907336705-21.686163892613.401747081273.4927658933
232.142153081110.3317352972130.9489615668651.934897218391.237049640811.783681361540.0524189413508-0.375528382107-0.05276161064230.268711112416-0.0303496529746-0.1405795894550.139602367774-0.274475478028-0.2453232923380.385327227579-0.203445247049-0.1190156780340.313587129347-0.1016888940480.13709221921113.279482589223.504195609746.9548724887
241.739475179050.418018520022-0.3849499164940.592613860516-0.6440508415690.7474309526380.2956511797170.339413293828-0.00362848441058-0.2546019251960.01949672499340.09233829559650.165121188594-0.07989382332270.4265020336930.596681437185-0.128079562817-0.1434285009380.127358341830.1646005665640.15004280385128.77176083536.528774745432.9518912702
253.157784297740.7287951776110.2457346424610.520198995921-0.1443512000011.8076006124-0.0226382814284-0.5865326375820.05358825259630.389792714767-0.133707322526-0.118614854311-0.305724700795-0.228741191093-0.1574229855010.506194030572-0.0615485678007-0.1618122227750.2360089006340.06381797299650.21790048630128.990809067635.721317852239.2213290538
267.44969638121.45642235131-2.641036770812.33842993967-1.36503464891.67516423242-0.249388623226-0.1231292385370.1185087904610.272702638766-0.0669935982419-0.407326546911-0.265353661891-0.000442890031173-0.2026663198880.481236079703-0.00645093018405-0.105323806690.191210931489-0.06989790360460.081842560653949.312995034343.33353117626.5089278236
273.974541150450.482368173788-1.555125098021.99116601007-0.130079603712.79683417395-0.1467797270870.743415298455-0.389945758519-0.283031359522-0.0261256999883-0.016589083206-0.299125077561-0.439914505136-0.02483019237110.432803014255-0.191963289211-0.09116133083870.308143290160.09668895866990.44494723185255.389972412737.369446149813.0290120594
282.066150013550.423074774630.6061117634691.367857731120.1875547674860.7948910697370.209616682002-0.087403633050.08315045816030.102801615777-0.214689317754-0.01424156451320.2310745852830.0604616063734-0.1195675745310.528049875649-0.086001892099-0.09198724564090.157487516644-0.05013866958330.473605977786-26.0687562764-35.497375772537.1365592163
294.610600385351.485516643122.231697274321.054991434230.9770679073851.787018967330.233253372599-0.315497986407-0.167084476260.215492391982-0.1779734840350.09863875935260.516221603528-0.341777528073-0.4761892379980.620428607938-0.218839442744-0.1777338926320.1792285985520.0003061178913940.115833505167-46.2948988623-42.318934006326.7678398883
302.927461938740.5624916606920.05580786050311.653308202770.5677939036631.741319147590.1244560663540.2895878643290.192480591243-0.112658076278-0.1749728504040.0477400751840.0812875345385-0.133710082196-0.02029117485720.41216431388-0.101759374014-0.03285974253940.1328021037350.0544258105860.411573964428-52.7746664325-35.08899602413.4693042457
313.348229570850.154544439868-1.011039762682.751512761480.2836596487391.6029559931-0.4841554256230.181211506523-0.503031517324-0.1049958176710.221459908510.3847867714450.545203425777-0.1039668338850.1107769592830.466739921157-0.00208140672605-0.1082968742330.209985748528-0.01427413182950.56291696353225.11122678314.946514648828.3459331509
322.066513388610.260846225187-1.252661868391.612344125840.1202297751521.20051003058-0.1424160838480.410716769406-0.5275245283210.1308650904050.0362418144245-0.07519809488110.3377105355470.04380978064280.1065375903880.336374253540.0505794159746-0.01385110669510.293499322047-0.04763941722380.52017774626128.441689972414.765280962925.06585277
332.40799107430.658000580026-0.1615380109772.22521273935-0.03051563336831.01690321673-0.03495877400050.123619315978-0.3709959627770.0185427294545-0.164176032493-0.3653714376470.2057640813540.0212739109928-0.002511231906310.324468502927-0.03031037328950.03199412814460.193624500553-0.1079222871710.37038204150255.121474529124.754313625418.6166107185
341.0987975185-0.0461041108504-0.3926010284011.97058004310.0389647854582.01123586668-0.04815611614360.484483835016-0.847640686909-0.439119047686-0.194518062999-0.296838190140.384508743249-0.2242897485760.1448434045490.604854006347-0.07248104471220.06977343985050.318801909306-0.1487903649470.73015821561149.20859495459.5098451930412.4848521303
350.270556666508-0.42132667284-0.1402946677541.678986323320.9042698213370.5319307512370.03031003302990.04411480442110.374851107524-0.175176107007-0.16679176697-0.257897998451-0.659560718143-0.131843528247-0.2026291151170.6295652211690.0221007613657-0.1811152085480.0735528734843-0.1938085258220.998114913539-26.7307859104-12.267271371329.5846322934
361.659409251060.167223806434-0.2643435871581.60464664547-0.5701391224340.9584403580790.06801556032290.1539839662-0.0648944416266-0.201952655321-0.108899709243-0.538812531537-0.2396663985840.3352223093050.0370043551480.548002885364-0.1412339112540.08885824579820.216810434395-0.03979706092480.783199746666-15.6189108899-17.095894426530.5303191353
370.5377673852490.427938260596-0.1459377621961.78428480609-0.5380788928190.975402518941-0.425071680433-0.008633275904990.112585132801-0.1036381172440.0167532270032-0.182476141667-0.128414601625-0.03066016730180.1198399835330.806996155912-0.00944243084157-0.2508455873930.1505938082230.002318237294290.976615823986-20.269013921-10.041844360927.602616795
380.3828743831920.0001460733142710.04058294677010.6460054530560.02423192815670.8442025624180.0659455851007-0.131829415950.260349514230.37896528055-0.139341672030.00880869140902-0.272357106764-0.000949910892605-0.1044008810180.523771258878-0.1092842747790.06183447909360.0735081303496-0.1518305193040.632050706423-25.6900662341-19.734817558636.7816752259
390.1052530445970.105458179046-0.09787365901570.312866758726-0.05218336704280.0935012689743-0.04654764768340.01492187672530.188327537014-0.01338229369060.08684891206320.01163820171080.01168497368410.01016783424870.2375825399140.6462495293830.0342388000457-0.2125975451730.03622546356320.1194481877140.789781708096-33.972447449-12.451773381911.5987190865
401.804683706261.19736565251-0.4712701534883.027261658560.1483067483211.17031847146-0.04522144092240.1193086178340.2329091308930.03325193432660.02545068251630.7580573340150.154624713138-0.324526452617-0.4092371127290.440323839705-0.0849240405011-0.1389421546240.3157829092880.1724127894520.452473004521-58.2746307416-27.741196851917.4442111914
410.7550876542250.5766484952630.6562496104421.7094240193-0.7074300127641.71925273685-0.0780232273851-0.08847876727730.4316362140370.18549403836-0.3580327107560.371794462553-0.004909212652360.0425973971008-0.1254594179220.617387024978-0.0226279816493-0.03825292066820.131412328065-0.04320734104350.667535701654-48.7584214801-19.604382992625.3490562732
421.52983752727-0.762318726085-0.4222869587761.70961405883-0.8925076948615.5354361486-0.09742257977540.2037458014990.69002649228-0.316222266306-0.439121999692-0.386312641627-0.009735323360090.4734413930760.04814664582630.575178929599-0.03262182368590.05834344434020.2499473906020.09466686848520.649179448619-38.0442248744-23.866609242410.9244493659
430.3667330167160.2895828408270.2823619161410.3922575501920.3265051134440.2637448649570.111549557434-0.06292337509760.3329217008540.290290127083-0.2836304146240.585022688707-0.0269068266964-0.163072806275-0.4759965835360.857997951107-0.0151195698375-0.06259214013960.0606006610541-0.02639029022760.624652914168-57.3993781741-22.443126728723.1778236544
440.2777623261180.0570270200654-0.05375089505131.24098987773-0.1765489714330.491001498449-0.2960780000110.07862254609240.4091964964240.04420655143840.01601100582750.121692079547-0.0397926188409-0.0595475291509-0.3716395603840.76907991894-0.0605225096337-0.2368161460550.05467590387690.07178813062790.947321063482-46.3578487853-8.0527429519614.4610627603
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 174 )AA1 - 1741 - 174
22chain 'A' and (resid 175 through 274 )AA175 - 274175 - 271
33chain 'B' and (resid 1 through 19 )BB1 - 191 - 19
44chain 'B' and (resid 20 through 43 )BB20 - 4320 - 43
55chain 'B' and (resid 44 through 53 )BB44 - 5344 - 53
66chain 'B' and (resid 54 through 71 )BB54 - 7154 - 71
77chain 'B' and (resid 72 through 99 )BB72 - 9972 - 99
88chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
99chain 'D' and (resid 1 through 37 )DD1 - 371 - 37
1010chain 'D' and (resid 38 through 56 )DD38 - 5638 - 56
1111chain 'D' and (resid 57 through 118 )DD57 - 11857 - 118
1212chain 'D' and (resid 119 through 137 )DD119 - 137119 - 137
1313chain 'D' and (resid 138 through 174 )DD138 - 174138 - 174
1414chain 'D' and (resid 175 through 230 )DD175 - 230175 - 230
1515chain 'D' and (resid 231 through 250 )DD231 - 250231 - 250
1616chain 'D' and (resid 251 through 274 )DD251 - 274251 - 274
1717chain 'E' and (resid 1 through 8 )EE1 - 81 - 8
1818chain 'E' and (resid 9 through 53 )EE9 - 539 - 53
1919chain 'E' and (resid 54 through 71 )EE54 - 7154 - 71
2020chain 'E' and (resid 72 through 77 )EE72 - 7772 - 77
2121chain 'E' and (resid 78 through 90 )EE78 - 9078 - 90
2222chain 'E' and (resid 91 through 99 )EE91 - 9991 - 99
2323chain 'F' and (resid 1 through 9 )FF1 - 91 - 9
2424chain 'G' and (resid 1 through 49 )GG1 - 491 - 43
2525chain 'G' and (resid 50 through 121 )GG50 - 12144 - 101
2626chain 'G' and (resid 122 through 135 )GG122 - 135102 - 115
2727chain 'G' and (resid 136 through 218 )GG136 - 218116 - 198
2828chain 'I' and (resid 1 through 121 )IH1 - 1211 - 101
2929chain 'I' and (resid 122 through 135 )IH122 - 135102 - 115
3030chain 'I' and (resid 136 through 219 )IH136 - 219116 - 199
3131chain 'H' and (resid 3 through 75 )HI3 - 751 - 61
3232chain 'H' and (resid 76 through 136 )HI76 - 13662 - 119
3333chain 'H' and (resid 137 through 227 )HI137 - 227120 - 210
3434chain 'H' and (resid 228 through 256 )HI228 - 256211 - 239
3535chain 'J' and (resid 3 through 44 )JJ3 - 441 - 35
3636chain 'J' and (resid 45 through 75 )JJ45 - 7536 - 61
3737chain 'J' and (resid 76 through 99 )JJ76 - 9962 - 84
3838chain 'J' and (resid 100 through 121 )JJ100 - 12185 - 104
3939chain 'J' and (resid 122 through 136 )JJ122 - 136105 - 119
4040chain 'J' and (resid 137 through 163 )JJ137 - 163120 - 146
4141chain 'J' and (resid 164 through 184 )JJ164 - 184147 - 167
4242chain 'J' and (resid 185 through 200 )JJ185 - 200168 - 183
4343chain 'J' and (resid 201 through 227 )JJ201 - 227184 - 210
4444chain 'J' and (resid 228 through 256 )JJ228 - 256211 - 239

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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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