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- PDB-3pqy: Crystal Structure of 6218 TCR in complex with the H2Db-PA224 -

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Basic information

Entry
Database: PDB / ID: 3pqy
TitleCrystal Structure of 6218 TCR in complex with the H2Db-PA224
Components
  • (T cell receptor ...) x 2
  • 10-mer peptide from RNA-directed RNA polymerase
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / H2Db / influenza / TCR / T cell / PA epitope / repertoire / viral immunity / chimeric TCR
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / endonuclease activity / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / Hydrolases; Acting on ester bonds / learning or memory / cell surface receptor signaling pathway / immune response / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / signaling receptor binding / DNA-templated transcription / host cell nucleus / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / metal ion binding / plasma membrane / cytosol
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 21-DV12 / T cell receptor beta, variable 29 / Human nkt tcr beta chain / T-cell receptor, sp3.4 alpha chain / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Polymerase acidic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.192 Å
AuthorsGras, S. / Guillonneau, C. / Turner, S.J. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for enabling T-cell receptor diversity within biased virus-specific CD8+ T-cell responses
Authors: Day, E.B. / Guillonneau, C. / Gras, S. / La Gruta, N.L. / Vignali, D.A.A. / Doherty, P.C. / Purcell, A.W. / Rossjohn, J. / Turner, S.J.
History
DepositionNov 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 12, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_entity_src_syn.details ..._entity.pdbx_description / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.5Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from RNA-directed RNA polymerase
D: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
E: T cell receptor beta, variable 29,Human nkt tcr beta chain
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: 10-mer peptide from RNA-directed RNA polymerase
I: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
J: T cell receptor beta, variable 29,Human nkt tcr beta chain
K: H-2 class I histocompatibility antigen, D-B alpha chain
L: Beta-2-microglobulin
M: 10-mer peptide from RNA-directed RNA polymerase
N: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
O: T cell receptor beta, variable 29,Human nkt tcr beta chain
P: H-2 class I histocompatibility antigen, D-B alpha chain
Q: Beta-2-microglobulin
R: 10-mer peptide from RNA-directed RNA polymerase
S: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
T: T cell receptor beta, variable 29,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)376,42920
Polymers376,42920
Non-polymers00
Water28816
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from RNA-directed RNA polymerase
D: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
E: T cell receptor beta, variable 29,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)94,1075
Polymers94,1075
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: 10-mer peptide from RNA-directed RNA polymerase
I: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
J: T cell receptor beta, variable 29,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)94,1075
Polymers94,1075
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: H-2 class I histocompatibility antigen, D-B alpha chain
L: Beta-2-microglobulin
M: 10-mer peptide from RNA-directed RNA polymerase
N: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
O: T cell receptor beta, variable 29,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)94,1075
Polymers94,1075
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: H-2 class I histocompatibility antigen, D-B alpha chain
Q: Beta-2-microglobulin
R: 10-mer peptide from RNA-directed RNA polymerase
S: T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain
T: T cell receptor beta, variable 29,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)94,1075
Polymers94,1075
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.893, 199.063, 202.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules AFKPBGLQ

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32030.648 Da / Num. of mol.: 4 / Fragment: UNP residues 26-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887

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T cell receptor ... , 2 types, 8 molecules DINSEJOT

#4: Protein
T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain / alpha chain of the 6218-TCR


Mass: 21609.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: chimeric construct with mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav21-dv12 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A075B6C4, UniProt: K7N5N2
#5: Protein
T cell receptor beta, variable 29,Human nkt tcr beta chain / beta chain of the 6218-TCR


Mass: 27575.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: chimeric construct with mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trbv29, B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0G2LB96, UniProt: K7N5M4

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Protein/peptide / Non-polymers , 2 types, 20 molecules CHMR

#3: Protein/peptide
10-mer peptide from RNA-directed RNA polymerase


Mass: 1186.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P13175*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE OF ENTITY 3 IS THE SAME AS RESIDUES 224-233 OF POLYMERASE FROM INFLUENZA A VIRUS.

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 10-14% PEG 3350, 0.2M KCN, 0.1M Bis Tris Propane pH 6.8, 5% glycerol, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.954 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.192→100 Å / Num. obs: 70035 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rsym value: 0.096 / Net I/σ(I): 12.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1YN6 and 1KGC

1yn6

1kgc


Resolution: 3.192→49.608 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.47 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3161 3538 5.06 %
Rwork0.2457 --
obs0.2493 69866 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.468 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 348.23 Å2 / Biso mean: 86.9781 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-5.0712 Å2-0 Å20 Å2
2---16.6424 Å2-0 Å2
3---11.5712 Å2
Refinement stepCycle: LAST / Resolution: 3.192→49.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25940 0 0 16 25956

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