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- PDB-8jv0: Crystal structure of the SLA-2*1001 allele and ASFV antigenic pep... -

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Basic information

Entry
Database: PDB / ID: 8jv0
TitleCrystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR
KeywordsIMMUNE SYSTEM / SLA / MHC I / IMMUNOLOGY ANTIGEN
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 / 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 ...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 / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / extracellular space / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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)
Asfivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution
Authors: Wang, S.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR
D: MHC class I antigen
E: Beta-2-microglobulin
F: TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR


Theoretical massNumber of molelcules
Total (without water)88,5646
Polymers88,5646
Non-polymers00
Water1,964109
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR


Theoretical massNumber of molelcules
Total (without water)44,2823
Polymers44,2823
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-22 kcal/mol
Surface area18990 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR


Theoretical massNumber of molelcules
Total (without water)44,2823
Polymers44,2823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-20 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.944, 105.317, 221.350
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 MHC class I antigen


Mass: 31759.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: B1A9P1
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11431.918 Da / Num. of mol.: 2
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 TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR


Mass: 1091.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Asfivirus
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate,0.1 M TRIS hydrochloride pH 8.5,30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 39759 / % possible obs: 98.4 % / Redundancy: 9.5 % / Rpim(I) all: 0.0267 / Net I/av σ(I): 0.25 / Net I/σ(I): 6
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 0.25 / Num. unique obs: 3586 / Rsym value: 0.562

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.03 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.797 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24882 1859 5 %RANDOM
Rwork0.22182 ---
obs0.22319 35066 72.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.232 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0 Å20 Å2
2--1.58 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 0 109 6333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136396
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175575
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6538678
X-RAY DIFFRACTIONr_angle_other_deg1.2461.58212978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53222.1400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.916151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.91552
X-RAY DIFFRACTIONr_chiral_restr0.0740.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7613.2823046
X-RAY DIFFRACTIONr_mcbond_other2.7613.2823045
X-RAY DIFFRACTIONr_mcangle_it4.4434.9113797
X-RAY DIFFRACTIONr_mcangle_other4.4424.9113798
X-RAY DIFFRACTIONr_scbond_it2.9033.6053350
X-RAY DIFFRACTIONr_scbond_other2.9023.6053350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8555.2554881
X-RAY DIFFRACTIONr_long_range_B_refined7.01835.436748
X-RAY DIFFRACTIONr_long_range_B_other7.01835.4276748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 41 -
Rwork0.305 769 -
obs--21.95 %

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