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- PDB-43sk: Crystal structure of H2-Q9/VP2.139 peptide H1A mutant -

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Basic information

Entry
Database: PDB / ID: 43sk
TitleCrystal structure of H2-Q9/VP2.139 peptide H1A mutant
Components
  • Beta-2-microglobulin
  • Histocompatibility 2, Q region locus 7
  • Minor capsid protein VP2
KeywordsIMMUNE SYSTEM / MHC / Viral / Non-classical / Antigen
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 / regulation of membrane depolarization / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation ...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 / regulation of membrane depolarization / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / iron ion transport / peptide antigen assembly with MHC class I protein complex / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / viral penetration into host nucleus / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / T cell differentiation in thymus / viral capsid / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / negative regulation of neuron projection development / host cell / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / antibacterial humoral response / protein refolding / amyloid fibril formation / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / host cell endoplasmic reticulum membrane / external side of plasma membrane / innate immune response / lysosomal membrane / symbiont entry into host cell / host cell nucleus / Golgi apparatus / structural molecule activity / protein homodimerization activity / : / DNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Polyomavirus coat protein VP2 / Polyomavirus coat protein / 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 / : ...Polyomavirus coat protein VP2 / Polyomavirus coat protein / 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 / Minor capsid protein VP2 / Histocompatibility 2, Q region locus 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Alphapolyomavirus muris
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsTennant, L. / Jobichen, C. / Tran, M.T. / Littler, D.R. / Farenc, C. / Gras, S. / Lukacher, A.E. / Sullivan, L.C. / Brooks, A.G. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: A murine MHC-Ib molecule, H2-Q9, drives peptide-centric T cell receptor recognition of a viral antigen
Authors: Tennant, L. / Jobichen, C. / Tran, M.T. / Littler, D.R. / Farenc, C. / Gras, S. / Lukacher, A.E. / Sullivan, L.C. / Brooks, A.G. / Rossjohn, J.
History
DepositionJul 15, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histocompatibility 2, Q region locus 7
B: Beta-2-microglobulin
P: Minor capsid protein VP2


Theoretical massNumber of molelcules
Total (without water)44,8343
Polymers44,8343
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-21 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.619, 56.799, 119.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histocompatibility 2, Q region locus 7 / MHC class Ib antigen


Mass: 31973.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Q9, H2-Q7 / Plasmid: pET-30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q52PG7
#2: Protein Beta-2-microglobulin


Mass: 11835.555 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 BL21(DE3) (bacteria) / References: UniProt: P01887
#3: Protein/peptide Minor capsid protein VP2 / Minor structural protein VP2


Mass: 1025.137 Da / Num. of mol.: 1 / Mutation: H1A / Source method: obtained synthetically / Source: (synth.) Alphapolyomavirus muris / References: UniProt: P03097
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium acetate, 0.1M HEPES pH 7.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.03→41.14 Å / Num. obs: 24708 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 16
Reflection shellResolution: 2.03→2.08 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 24708 / CC1/2: 0.754 / Rpim(I) all: 0.302

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→41.14 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1256 5.09 %
Rwork0.2088 --
obs0.2106 24655 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 124 3266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023248
X-RAY DIFFRACTIONf_angle_d0.5164414
X-RAY DIFFRACTIONf_dihedral_angle_d17.6671198
X-RAY DIFFRACTIONf_chiral_restr0.042448
X-RAY DIFFRACTIONf_plane_restr0.004576

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