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- PDB-8gqv: The Crystal Structures of a Swine SLA-2*HB01 Molecules Complexed ... -

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Basic information

Entry
Database: PDB / ID: 8gqv
TitleThe Crystal Structures of a Swine SLA-2*HB01 Molecules Complexed with a CTL epitope from Asia1 serotype of Foot-and-mouth disease virus
Components
  • As64
  • MHC class I antigen
  • beta 2 microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM/EPITOPE / SLA-2 / foot-and-mouth disease virus / crystal / peptide / epitope / CTL / Complex / Peptide presentation / universal vaccine candidate / IMMUNE SYSTEM / IMMUNE SYSTEM-EPITOPE complex
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 / MHC class I 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 / antigen processing and presentation / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / 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)
Foot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFeng, L. / Gao, Y.Y. / Sun, M.W. / Li, Z.B. / Zhang, Q. / Yang, J. / Qiao, C. / Jin, H. / Feng, H.S. / Xian, Y.H. ...Feng, L. / Gao, Y.Y. / Sun, M.W. / Li, Z.B. / Zhang, Q. / Yang, J. / Qiao, C. / Jin, H. / Feng, H.S. / Xian, Y.H. / Qi, J.X. / Gao, G.F. / Liu, W.J. / Gao, F.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31172304 and 31672525 China
CitationJournal: Cells / Year: 2022
Title: The Parallel Presentation of Two Functional CTL Epitopes Derived from the O and Asia 1 Serotypes of Foot-and-Mouth Disease Virus and Swine SLA-2*HB01: Implications for Universal Vaccine Development.
Authors: Feng, L. / Gao, Y.Y. / Sun, M. / Li, Z.B. / Zhang, Q. / Yang, J. / Qiao, C. / Jin, H. / Feng, H.S. / Xian, Y.H. / Qi, J. / Gao, G.F. / Liu, W.J. / Gao, F.S.
History
DepositionAug 31, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: As64
D: MHC class I antigen
E: beta 2 microglobulin
F: As64


Theoretical massNumber of molelcules
Total (without water)88,4726
Polymers88,4726
Non-polymers00
Water3,603200
1
A: MHC class I antigen
B: beta 2 microglobulin
C: As64


Theoretical massNumber of molelcules
Total (without water)44,2363
Polymers44,2363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-17 kcal/mol
Surface area18930 Å2
MethodPISA
2
D: MHC class I antigen
E: beta 2 microglobulin
F: As64


Theoretical massNumber of molelcules
Total (without water)44,2363
Polymers44,2363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-14 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.465, 98.143, 166.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 31746.020 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: E3WHS2
#2: Protein beta 2 microglobulin / Beta-2 microglobulin


Mass: 11431.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717
#3: Protein/peptide As64


Mass: 1058.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate, PEG, BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MAATEL IMAGINE / Detector: IMAGE PLATE / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31827 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 33.63 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.318 / Num. unique obs: 31827

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q94

1q94


Resolution: 2.4→48.202 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1596 5.05 %
Rwork0.2045 30002 -
obs0.2069 31598 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.75 Å2 / Biso mean: 46.2 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 2.4→48.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 0 200 6436
Biso mean---41.25 -
Num. residues----764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056408
X-RAY DIFFRACTIONf_angle_d1.0038692
X-RAY DIFFRACTIONf_chiral_restr0.07888
X-RAY DIFFRACTIONf_plane_restr0.0041146
X-RAY DIFFRACTIONf_dihedral_angle_d15.9962378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.490.19531470.1903292499
2.4003-2.47780.3411450.2568260998
2.4778-2.56640.30021240.2408269298
2.5664-2.66910.30431270.2354267899
2.6691-2.79060.32091600.23962671100
2.7906-2.93770.27011580.23332689100
2.9377-3.12170.30251470.23632718100
3.1217-3.36270.28881520.21772710100
3.3627-3.7010.28211290.19272765100
3.701-4.23620.20681590.18772749100
4.2362-5.33610.1931480.16632797100
Refinement TLS params.Method: refined / Origin x: -12.7487 Å / Origin y: -41.0208 Å / Origin z: 14.1495 Å
111213212223313233
T0.1578 Å2-0.0089 Å2-0.0173 Å2-0.1681 Å20.0222 Å2--0.1842 Å2
L0.0408 °2-0.0159 °2-0.022 °2-0.2024 °20.2728 °2--0.5054 °2
S-0.0218 Å °0.013 Å °0.0073 Å °-0.0111 Å °-0.0116 Å °0.0004 Å °-0.0482 Å °0.016 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 275
2X-RAY DIFFRACTION1allB1 - 98
3X-RAY DIFFRACTION1allC1 - 9
4X-RAY DIFFRACTION1allD1 - 275
5X-RAY DIFFRACTION1allE1 - 98
6X-RAY DIFFRACTION1allF1 - 9
7X-RAY DIFFRACTION1allS1 - 200

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