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- PDB-8w6l: Crystal structure of the SLA-2*1001 allele and ASFV antigenic pep... -

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Basic information

Entry
Database: PDB / ID: 8w6l
TitleCrystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • THR-MET-TYR-SER-LEU-GLY-TYR-ILE-PHE
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 Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...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 Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / 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 / : ...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: 2.03 Å
AuthorsWang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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
DepositionAug 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: THR-MET-TYR-SER-LEU-GLY-TYR-ILE-PHE


Theoretical massNumber of molelcules
Total (without water)44,2853
Polymers44,2853
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-18 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.531, 48.883, 51.173
Angle α, β, γ (deg.)94.40, 101.86, 100.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MHC class I antigen


Mass: 31759.047 Da / Num. of mol.: 1
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.: 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 THR-MET-TYR-SER-LEU-GLY-TYR-ILE-PHE


Mass: 1094.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Asfivirus
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium thiocyanate,20% w/v Polyethylene glycol 3,350,pH 6.9

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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 4, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.029→49.72 Å / Num. obs: 24852 / % possible obs: 97.971 % / Redundancy: 1 % / Rmerge(I) obs: 0.022 / Net I/σ(I): 2.44
Reflection shellResolution: 2.3→2.58 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.78 / Num. unique obs: 1790 / Rpim(I) all: 0.142

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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: 2.03→49.72 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.823 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27652 1281 5.3 %RANDOM
Rwork0.2376 ---
obs0.23964 23024 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0.63 Å20.54 Å2
2--1.43 Å2-2.25 Å2
3---0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.03→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 0 67 3159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133188
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172787
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6524323
X-RAY DIFFRACTIONr_angle_other_deg1.2311.5816483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8745377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59422.01199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76815526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7661526
X-RAY DIFFRACTIONr_chiral_restr0.070.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it2.8643.8151517
X-RAY DIFFRACTIONr_mcbond_other2.8543.8151516
X-RAY DIFFRACTIONr_mcangle_it4.4225.7161891
X-RAY DIFFRACTIONr_mcangle_other4.4215.7151892
X-RAY DIFFRACTIONr_scbond_it3.2184.1161671
X-RAY DIFFRACTIONr_scbond_other3.2174.1151672
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0686.042433
X-RAY DIFFRACTIONr_long_range_B_refined7.42742.0883437
X-RAY DIFFRACTIONr_long_range_B_other7.42642.0753436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.039→2.082 Å
RfactorNum. reflection% reflection
Rfree0.364 75 -
Rwork0.364 1692 -
obs--96.03 %

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