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- PDB-7jwj: Crystal Structure of B17-C1 TCR-H2Db -

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Basic information

Entry
Database: PDB / ID: 7jwj
TitleCrystal Structure of B17-C1 TCR-H2Db
Components
  • B17.C1 TCR alpha chain
  • B17.C1 TCR beta chain
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / TCR / MHC / Complex
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 / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / helical viral capsid / 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 Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / viral penetration into host nucleus / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / host cell / 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 / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / symbiont entry into host cell / ribonucleoprotein complex / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.251 Å
AuthorsFarenc, C. / Rossjohn, J. / Gras, S. / Szeto, C.
CitationJournal: Science / Year: 2021
Title: Canonical T cell receptor docking on peptide-MHC is essential for T cell signaling.
Authors: Zareie, P. / Szeto, C. / Farenc, C. / Gunasinghe, S.D. / Kolawole, E.M. / Nguyen, A. / Blyth, C. / Sng, X.Y.X. / Li, J. / Jones, C.M. / Fulcher, A.J. / Jacobs, J.R. / Wei, Q. / Wojciech, L. ...Authors: Zareie, P. / Szeto, C. / Farenc, C. / Gunasinghe, S.D. / Kolawole, E.M. / Nguyen, A. / Blyth, C. / Sng, X.Y.X. / Li, J. / Jones, C.M. / Fulcher, A.J. / Jacobs, J.R. / Wei, Q. / Wojciech, L. / Petersen, J. / Gascoigne, N.R.J. / Evavold, B.D. / Gaus, K. / Gras, S. / Rossjohn, J. / La Gruta, N.L.
History
DepositionAug 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Apr 24, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Nucleoprotein
D: B17.C1 TCR alpha chain
E: B17.C1 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)106,3245
Polymers106,3245
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-41 kcal/mol
Surface area39990 Å2
Unit cell
Length a, b, c (Å)61.769, 224.636, 172.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 4 types, 4 molecules ABDE

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


Mass: 40885.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 13796.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#4: Protein B17.C1 TCR alpha chain


Mass: 22591.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Protein B17.C1 TCR beta chain


Mass: 28023.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein/peptide / Non-polymers , 2 types, 11 molecules C

#3: Protein/peptide Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 1026.099 Da / Num. of mol.: 1 / Fragment: NP-366 epitope (UNP residues 366-374) / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q9Q0U8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 16% PEG3350, 0.2 M potassium thiocyanide, 4% ethylene glycol, 0.1 M Bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.25→47.65 Å / Num. obs: 19231 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 99.31 Å2 / CC1/2: 1 / Net I/σ(I): 13.87
Reflection shellResolution: 3.25→3.37 Å / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1862 / CC1/2: 0.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (20-MAY-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5SWZ

5swz


Resolution: 3.251→47.65 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.57
RfactorNum. reflection% reflectionSelection details
Rfree0.3062 952 4.95 %RANDOM
Rwork0.2756 ---
obs0.2771 19231 99.3 %-
Displacement parametersBiso max: 242.99 Å2 / Biso mean: 123.3 Å2 / Biso min: 49.97 Å2
Baniso -1Baniso -2Baniso -3
1-28.7311 Å20 Å20 Å2
2---30.1657 Å20 Å2
3---1.4346 Å2
Refine analyzeLuzzati coordinate error obs: 0.63 Å
Refinement stepCycle: final / Resolution: 3.251→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 0 10 6552
Biso mean---68.25 -
Num. residues----811
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3076SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1147HARMONIC5
X-RAY DIFFRACTIONt_it6732HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion849SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4117SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6732HARMONIC20.004
X-RAY DIFFRACTIONt_angle_deg9133HARMONIC20.61
X-RAY DIFFRACTIONt_omega_torsion1.87
X-RAY DIFFRACTIONt_other_torsion2.95
LS refinement shellResolution: 3.251→3.28 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4037 16 3.9 %
Rwork0.2853 394 -
obs--98.53 %

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