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- PDB-5e6i: Crystal structure of TCR PF8 in complex with flu MP(58-66) epitop... -

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Entry
Database: PDB / ID: 5e6i
TitleCrystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Matrix protein 1
  • T-cell receptor beta-2 chain C region
  • TCR alpha chain,Human nkt tcr alpha chain
KeywordsIMMUNE SYSTEM / TCR / HLA-A2 / Flu / Complex
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 / 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 / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / Viral mRNA Translation / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / viral budding from plasma membrane / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / structural constituent of virion / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / innate immune response
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 / : ...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 / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Similarity search - Domain/homology
: / Matrix protein 1 / Human nkt tcr alpha chain / 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: 4 Å
AuthorsGao, M. / Mariuzza, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI036900 United States
CitationJournal: To Be Published
Title: Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2
Authors: Gao, M.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 29, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: TCR alpha chain,Human nkt tcr alpha chain
H: T-cell receptor beta-2 chain C region
I: HLA class I histocompatibility antigen, A-2 alpha chain
J: Beta-2-microglobulin
K: Matrix protein 1
A: TCR alpha chain,Human nkt tcr alpha chain
B: T-cell receptor beta-2 chain C region
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
E: Matrix protein 1
F: TCR alpha chain,Human nkt tcr alpha chain
L: T-cell receptor beta-2 chain C region
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: Beta-2-microglobulin
O: Matrix protein 1
P: TCR alpha chain,Human nkt tcr alpha chain
Q: T-cell receptor beta-2 chain C region
R: HLA class I histocompatibility antigen, A-2 alpha chain
U: Beta-2-microglobulin
T: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)381,25620
Polymers381,25620
Non-polymers00
Water00
1
G: TCR alpha chain,Human nkt tcr alpha chain
H: T-cell receptor beta-2 chain C region
I: HLA class I histocompatibility antigen, A-2 alpha chain
J: Beta-2-microglobulin
K: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)95,3145
Polymers95,3145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TCR alpha chain,Human nkt tcr alpha chain
B: T-cell receptor beta-2 chain C region
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
E: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)95,3145
Polymers95,3145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: TCR alpha chain,Human nkt tcr alpha chain
L: T-cell receptor beta-2 chain C region
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: Beta-2-microglobulin
O: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)95,3145
Polymers95,3145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: TCR alpha chain,Human nkt tcr alpha chain
Q: T-cell receptor beta-2 chain C region
R: HLA class I histocompatibility antigen, A-2 alpha chain
U: Beta-2-microglobulin
T: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)95,3145
Polymers95,3145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.853, 123.614, 139.036
Angle α, β, γ (deg.)83.660, 74.870, 73.170
Int Tables number1
Space group name H-MP1
DetailsPentamer confirmed by chromatography

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Components

#1: Protein
TCR alpha chain,Human nkt tcr alpha chain / Human nkt tcr beta chain


Mass: 22716.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Gene: B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: K7N5M3
#2: Protein
T-cell receptor beta-2 chain C region


Mass: 27767.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBC2 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A087WZ08
#3: Protein
HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31985.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#4: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61769
#5: Protein/peptide
Matrix protein 1


Mass: 966.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: E9P5U1, UniProt: P03485*PLUS
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M immidazole pH8, 0.2M calcium acetate, 10%(v/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4→46.16 Å / Num. obs: 34067 / % possible obs: 91.5 % / Redundancy: 2.05 % / Biso Wilson estimate: 111.85 Å2 / Rmerge(I) obs: 0.164 / Χ2: 0.98 / Net I/σ(I): 2.9 / Num. measured all: 70283 / Scaling rejects: 528
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
4-4.142.080.5731699233431.152391.3
4.14-4.312.060.4831.3689933461.081989.6
4.31-4.52.050.4041.6690933561.061690.1
4.5-4.742.040.3561.8700734220.992791.4
4.74-5.042.010.3331.9684833780.984291.1
5.04-5.431.990.3232680033980.994591.1
5.43-5.972.050.3112.2702633990.964290.5
5.97-6.832.060.2832.4706333980.975892.1
6.83-8.62.080.1544.6751335750.898295.5
8.6-46.162.040.0849.6722634520.7517492.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
d*TREK9.9.8.6 W9RSSIdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLJ, 3VXT

2vlj

3vxt


Resolution: 4→36.562 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3376 1647 4.86 %Random selection
Rwork0.2591 32215 --
obs0.2626 33862 90.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.97 Å2 / Biso mean: 108.7672 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 4→36.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24882 0 0 0 24882
Num. residues----3204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825551
X-RAY DIFFRACTIONf_angle_d1.41634681
X-RAY DIFFRACTIONf_chiral_restr0.0583694
X-RAY DIFFRACTIONf_plane_restr0.0084549
X-RAY DIFFRACTIONf_dihedral_angle_d17.1639033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.11760.41961330.35572644277791
4.1176-4.25030.38711260.33852639276589
4.2503-4.40190.41531550.29582666282191
4.4019-4.57790.38451440.29162669281390
4.5779-4.78580.35011400.27052672281289
4.7858-5.03750.31521380.27152664280292
5.0375-5.35220.39671410.27212688282991
5.3522-5.7640.37551290.2792696282591
5.764-6.34130.3564930.29162723281691
6.3413-7.25270.36421570.2842753291093
7.2527-9.11420.28361700.22232800297096
9.1142-36.56360.24211210.17772601272288

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