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- PDB-5jhd: Crystal structure of LS10-TCR/M1-HLA-A*02 complex -

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基本情報

登録情報
データベース: PDB / ID: 5jhd
タイトルCrystal structure of LS10-TCR/M1-HLA-A*02 complex
要素
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Influenza M1(58-66) peptide
  • TCRalpha chain
  • TCRbeta chain
キーワードIMMUNE SYSTEM / TCR-HLA*A2 / M1 / influenza / matrix protein
機能・相同性
機能・相同性情報


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / Viral mRNA Translation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / : / : / viral budding from plasma membrane / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / 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 / structural constituent of virion / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen
類似検索 - 分子機能
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I, alpha chain, C-terminal ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Chem-EDT / HLA class I histocompatibility antigen, A alpha chain / Matrix protein 1 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.46 Å
データ登録者Stern, L.J. / Selin, L.K. / Song, I.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI038996 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109858 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI49320 米国
引用ジャーナル: Nat. Struct. Mol. Biol. / 年: 2017
タイトル: Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8(+) T cell epitope.
著者: Song, I. / Gil, A. / Mishra, R. / Ghersi, D. / Selin, L.K. / Stern, L.J.
履歴
登録2016年4月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年3月1日Provider: repository / タイプ: Initial release
改定 1.12017年3月15日Group: Database references
改定 1.22017年4月19日Group: Database references
改定 1.32017年9月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42019年5月8日Group: Data collection / Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
改定 1.52019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.62023年9月27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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.72024年11月6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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Influenza M1(58-66) peptide
D: TCRalpha chain
E: TCRbeta chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Influenza M1(58-66) peptide
I: TCRalpha chain
J: TCRbeta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)192,64212
ポリマ－192,05710
非ポリマー5842
水2,864159
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Influenza M1(58-66) peptide
D: TCRalpha chain
E: TCRbeta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,3216
ポリマ－96,0295
非ポリマー2921
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Influenza M1(58-66) peptide
I: TCRalpha chain
J: TCRbeta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,3216
ポリマ－96,0295
非ポリマー2921
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)49.710, 101.840, 113.550
Angle α, β, γ (deg.)99.380, 92.600, 103.450
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain D and ((resid 3 and (name O or name...
21(chain I and ((resid 3 and (name N or name...
12(chain A and (resseq 1:130 or resseq 132:156 or resseq...
22(chain F and (resseq 1:130 or resseq 132:156 or resseq...
13(chain E and (resseq 4:13 or (resid 14 and (name...
23(chain J and (resseq 4:13 or (resid 14 and (name...
14chain H
24chain C
15(chain B and (resseq 0:29 or (resid 30 and (name...
25(chain G and (resseq 0:29 or (resid 30 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRTHRTHR(chain D and ((resid 3 and (name O or name...DD34
121THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
131THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
141THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
151THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
161THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
171THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
181THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
191THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
1101THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
1111THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
1121THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
1131THRTHRSERSER(chain D and ((resid 3 and (name O or name...DD3 - 2084 - 209
211THRTHRTHRTHR(chain I and ((resid 3 and (name N or name...II34
221GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
231GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
241GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
251GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
261GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
271GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
281GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
291GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
2101GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
2111GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
2121GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
2131GLNGLNSERSER(chain I and ((resid 3 and (name N or name...II2 - 2083 - 209
112GLYGLYLEULEU(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 1301 - 130
122SERSERLEULEU(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA132 - 156132 - 156
132TYRTYRCYSCYS(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA159 - 203159 - 203
142TRPTRPTRPTRP(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA204204
152GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
162GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
172GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
182GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
192GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1102GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1112GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1122GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1132GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1142GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1152GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1162GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1172GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1182GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1192GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1202GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1212GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1222GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1232GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1242GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1252GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
1262GLYGLYALAALA(chain A and (resseq 1:130 or resseq 132:156 or resseq...AA1 - 2761 - 276
212GLYGLYLEULEU(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 1301 - 130
222SERSERLEULEU(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF132 - 156132 - 156
232TYRTYRCYSCYS(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF159 - 203159 - 203
242TRPTRPTRPTRP(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF204204
252GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
262GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
272GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
282GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
292GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2102GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2112GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2122GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2132GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2142GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2152GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2162GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2172GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2182GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2192GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2202GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2212GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2222GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2232GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2242GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2252GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
2262GLYGLYALAALA(chain F and (resseq 1:130 or resseq 132:156 or resseq...FF1 - 2761 - 276
113GLYGLYLEULEU(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 133 - 12
123PHEPHEPHEPHE(chain E and (resseq 4:13 or (resid 14 and (name...EE1413
133GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
143GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
153GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
163GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
173GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
183GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
193GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1103GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1113GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1123GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1133GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1143GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1153GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1163GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1173GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1183GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
1193GLYGLYALAALA(chain E and (resseq 4:13 or (resid 14 and (name...EE4 - 2423 - 241
213GLYGLYLEULEU(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 133 - 12
223PHEPHEPHEPHE(chain J and (resseq 4:13 or (resid 14 and (name...JJ1413
233GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
243GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
253GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
263GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
273GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
283GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
293GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2103GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2113GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2123GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2133GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2143GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2153GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2163GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2173GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2183GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
2193GLYGLYALAALA(chain J and (resseq 4:13 or (resid 14 and (name...JJ4 - 2423 - 241
114GLYGLYLEULEUchain HHH1 - 91 - 9
214GLYGLYLEULEUchain CCC1 - 91 - 9
115METMETGLYGLY(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 291 - 30
125PHEPHEPHEPHE(chain B and (resseq 0:29 or (resid 30 and (name...BB3031
135METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
145METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
155METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
165METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
175METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
185METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
195METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1105METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1115METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1125METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1135METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1145METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1155METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1165METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1175METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1185METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
1195METMETMETMET(chain B and (resseq 0:29 or (resid 30 and (name...BB0 - 991 - 100
215METMETGLYGLY(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 291 - 30
225PHEPHEPHEPHE(chain G and (resseq 0:29 or (resid 30 and (name...GG3031
235METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
245METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
255METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
265METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
275METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
285METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
295METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2105METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2115METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2125METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2135METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2145METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2155METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2165METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2175METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2185METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100
2195METMETMETMET(chain G and (resseq 0:29 or (resid 30 and (name...GG0 - 991 - 100

NCSアンサンブル:
ID
1
2
3
4
5

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要素

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タンパク質 , 4種, 8分子 AFBGDIEJ

#1: タンパク質 HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


分子量: 31925.281 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, HLAA / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P01892, UniProt: P04439*PLUS
#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) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P61769
#4: タンパク質 TCRalpha chain


分子量: 23849.352 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: TRA@ / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
#5: タンパク質 TCRbeta chain


分子量: 27408.543 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) / 株 (発現宿主): BL21(DE3)

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タンパク質・ペプチド , 1種, 2分子 CH

#3: タンパク質・ペプチド Influenza M1(58-66) peptide


分子量: 966.174 Da / 分子数: 2 / 由来タイプ: 合成
由来: (合成) Influenza A virus (A型インフルエンザウイルス)
参照: UniProt: P03485*PLUS

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非ポリマー , 2種, 161分子

#6: 化合物 ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID / EDTA


分子量: 292.243 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N2O8
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 159 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.86 Å3/Da / 溶媒含有率: 57.01 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 10%(W/V) PEG8000, 100mM Tris-Cl, 200mM Magnesium chloirde

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 31-ID / 波長: 0.9793 Å
検出器タイプ: RAYONIX MX225HE / 検出器: CCD / 日付: 2015年7月8日
放射モノクロメーター: Kohzu HLD-4 Double Crystal / 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: 0.9793 Å / 相対比: 1
反射解像度: 2.46→111.609 Å / Num. obs: 72668 / % possible obs: 94 % / 冗長度: 3.9 % / Rsym value: 0.116 / Net I/av σ(I): 5.242 / Net I/σ(I): 8.1
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.46-2.593.70.810.9172
2.59-2.753.80.651.1197.2
2.75-2.943.90.4061.8197.4
2.94-3.1840.2283.2197.6
3.18-3.4840.145.1197.8
3.48-3.8940.0956.9197.9
3.89-4.4940.0728.2198.2
4.49-5.540.0698.7198.4
5.5-7.7840.078.1198.5
7.78-80.9173.90.0569.8197.6

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation2.58 Å80.92 Å
Translation2.58 Å80.92 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
SCALA3.3.22データスケーリング
PHASER2.5.6位相決定
PDB_EXTRACT3.2データ抽出
iMOSFLMデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 1OGA

1oga


解像度: 2.46→29.051 Å / SU ML: 0.32 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 26.12
Rfactor反射数%反射
Rfree0.2233 3541 4.88 %
Rwork0.2043 --
obs0.2052 72567 93.93 %
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 max: 224.2 Å2 / Biso mean: 73.6158 Å2 / Biso min: 20 Å2
精密化ステップサイクル: final / 解像度: 2.46→29.051 Å
タンパク質核酸リガンド溶媒全体
原子数13282 0 64 159 13505
Biso mean--37.41 49.11 -
残基数----1652
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00313701
X-RAY DIFFRACTIONf_angle_d0.62118616
X-RAY DIFFRACTIONf_chiral_restr0.0431943
X-RAY DIFFRACTIONf_plane_restr0.0032436
X-RAY DIFFRACTIONf_dihedral_angle_d15.348112
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11D2138X-RAY DIFFRACTION6.166TORSIONAL
12I2138X-RAY DIFFRACTION6.166TORSIONAL
21A3388X-RAY DIFFRACTION6.166TORSIONAL
22F3388X-RAY DIFFRACTION6.166TORSIONAL
31E2708X-RAY DIFFRACTION6.166TORSIONAL
32J2708X-RAY DIFFRACTION6.166TORSIONAL
41H112X-RAY DIFFRACTION6.166TORSIONAL
42C112X-RAY DIFFRACTION6.166TORSIONAL
51B1300X-RAY DIFFRACTION6.166TORSIONAL
52G1300X-RAY DIFFRACTION6.166TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.49370.41561100.36461844195462
2.4937-2.52930.35841040.35321925202967
2.5293-2.5670.37191100.34362254236476
2.567-2.60710.30651250.32862720284591
2.6071-2.64980.2931410.3092823296497
2.6498-2.69550.33331520.3132831298397
2.6955-2.74450.35211470.29282883303097
2.7445-2.79720.25941670.27522828299597
2.7972-2.85430.26971360.26612853298997
2.8543-2.91630.26341380.25242937307598
2.9163-2.9840.3081570.24392788294598
2.984-3.05860.26121540.23882849300397
3.0586-3.14120.2781520.24042902305498
3.1412-3.23350.24841400.22342851299198
3.2335-3.33770.21691540.21622902305698
3.3377-3.45680.23861530.20642819297298
3.4568-3.5950.23051430.19682934307798
3.595-3.75830.18681580.18352852301098
3.7583-3.9560.20111310.18062889302098
3.956-4.20310.1961420.16122904304698
4.2031-4.52660.15931650.14452865303098
4.5266-4.980.17471360.13512908304498
4.98-5.69590.17011480.16012891303998
5.6959-7.15850.19811340.20092909304399
7.1585-29.05270.20371440.22865300998

+
万見について

-
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

-
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

+
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

+
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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