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

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Basic information

Entry
Database: PDB / ID: 5jhd
TitleCrystal structure of LS10-TCR/M1-HLA-A*02 complex
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Influenza M1(58-66) peptide
  • TCRalpha chain
  • TCRbeta chain
KeywordsIMMUNE SYSTEM / TCR-HLA*A2 / M1 / influenza / matrix protein
Function / homology
Function and homology information


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 / Viral mRNA Translation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane
Similarity search - Function
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-EDT / HLA class I histocompatibility antigen, A alpha chain / Matrix protein 1 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.46 Å
AuthorsStern, L.J. / Selin, L.K. / Song, I.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI038996 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109858 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI49320 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8(+) T cell epitope.
Authors: Song, I. / Gil, A. / Mishra, R. / Ghersi, D. / Selin, L.K. / Stern, L.J.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,64212
Polymers192,05710
Non-polymers5842
Water2,864159
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3216
Polymers96,0295
Non-polymers2921
Water905
TypeNameSymmetry operationNumber
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3216
Polymers96,0295
Non-polymers2921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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 domain segments:
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 ensembles :
ID
1
2
3
4
5

-
Components

-
Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31925.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein TCRalpha chain


Mass: 23849.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein TCRbeta chain


Mass: 27408.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

-
Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Influenza M1(58-66) peptide


Mass: 966.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: P03485*PLUS

-
Non-polymers , 2 types, 161 molecules

#6: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID / Ethylenediaminetetraacetic acid


Mass: 292.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O8
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10%(W/V) PEG8000, 100mM Tris-Cl, 200mM Magnesium chloirde

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 8, 2015
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.46→111.609 Å / Num. obs: 72668 / % possible obs: 94 % / Redundancy: 3.9 % / Rsym value: 0.116 / Net I/av σ(I): 5.242 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)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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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.58 Å80.92 Å
Translation2.58 Å80.92 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA

1oga


Resolution: 2.46→29.051 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2233 3541 4.88 %
Rwork0.2043 --
obs0.2052 72567 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 224.2 Å2 / Biso mean: 73.6158 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.46→29.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13282 0 64 159 13505
Biso mean--37.41 49.11 -
Num. residues----1652
Refine LS restraints
Refine-IDTypeDev idealNumber
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-IDNumberRefine-IDRmsType
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 refinement shell

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

Resolution (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

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