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- PDB-9ul1: Crystal structure of Tibetan wild boar SLA-1*Z0301 for 2.32 angstrom -

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Basic information

Entry
Database: PDB / ID: 9ul1
TitleCrystal structure of Tibetan wild boar SLA-1*Z0301 for 2.32 angstrom
Components
  • ALA-LEU-LEU-SER-SER-LYS-THR-SER-VAL
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsANTIVIRAL PROTEIN / MHC / Immunology / Immune system
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / extracellular region
Similarity search - Function
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 / : ...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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
Porcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.323 Å
AuthorsFan, S. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31702232 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural basis of Tibetan wild boar SLA-1*Z0301 reveals conserved peptide presentation and potential high-altitude adaptation.
Authors: Fan, S. / Kang, C. / Peng, J. / Wang, T. / Ren, S. / Li, J. / Li, L. / Wu, C. / Wang, Y. / Li, L.
History
DepositionApr 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ALA-LEU-LEU-SER-SER-LYS-THR-SER-VAL


Theoretical massNumber of molelcules
Total (without water)44,2153
Polymers44,2153
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: ALA-LEU-LEU-SER-SER-LYS-THR-SER-VAL

A: MHC class I antigen
B: Beta-2-microglobulin
C: ALA-LEU-LEU-SER-SER-LYS-THR-SER-VAL


Theoretical massNumber of molelcules
Total (without water)88,4306
Polymers88,4306
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area10940 Å2
ΔGint-43 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.806, 48.428, 53.419
Angle α, β, γ (deg.)90.000, 100.466, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31976.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Tibetan wild boar SLA-1*Z0301 complex with PRRSV peptide
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A286S063
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11332.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717
#3: Protein/peptide ALA-LEU-LEU-SER-SER-LYS-THR-SER-VAL


Mass: 906.057 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Porcine reproductive and respiratory syndrome virus
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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% [wt/vol] polyethylene glycol 3350, 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.32→46.246 Å / Num. obs: 15993 / % possible obs: 92.72 % / Redundancy: 3.3 % / Rpim(I) all: 0.041 / Net I/σ(I): 15.5
Reflection shellResolution: 2.32→2.38 Å / Num. unique obs: 2373 / Rpim(I) all: 0.537

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.323→46.246 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.888 / SU B: 0.1 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.31 / ESU R Free: 0.323
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.294 773 4.833 %
Rwork0.2779 15220 -
all0.283 --
obs-15993 92.718 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.809 Å2
Baniso -1Baniso -2Baniso -3
1-2.264 Å2-0 Å2-4.664 Å2
2--7.618 Å2-0 Å2
3----7.638 Å2
Refinement stepCycle: LAST / Resolution: 2.323→46.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 0 0 3118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.323-2.3830.392540.373980X-RAY DIFFRACTION84.7541
2.383-2.4480.459600.3611175X-RAY DIFFRACTION99.2765
2.448-2.5190.342580.261139X-RAY DIFFRACTION99.8332
2.519-2.5960.352570.2441095X-RAY DIFFRACTION99.9133
2.596-2.6810.331500.3181102X-RAY DIFFRACTION99.8267
2.681-2.7750.443590.3091015X-RAY DIFFRACTION99.4444
2.775-2.8790.307460.281997X-RAY DIFFRACTION99.7132
2.879-2.9970.356540.286979X-RAY DIFFRACTION99.3269
2.997-3.1290.283330.268909X-RAY DIFFRACTION98.8457
3.129-3.2810.303420.27876X-RAY DIFFRACTION96.7334
3.281-3.4580.278440.272790X-RAY DIFFRACTION93.3931
3.458-3.6660.271380.24692X-RAY DIFFRACTION88.6999
3.666-3.9170.268330.261655X-RAY DIFFRACTION85.0433
3.917-4.2290.275240.248580X-RAY DIFFRACTION81.9539
4.229-4.6290.269320.256451X-RAY DIFFRACTION70.7174
4.629-5.1680.261200.253425X-RAY DIFFRACTION70.9729
5.168-5.9560.274260.203449X-RAY DIFFRACTION83.9223
5.956-7.2640.307190.249409X-RAY DIFFRACTION92.4406
7.264-100.231120.226303X-RAY DIFFRACTION83.5544
8-100.355120.293199X-RAY DIFFRACTION92.1397

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