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- PDB-5h94: Crystal structure of Swine MHC CLASSI for 1.48 angstroms -

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Basic information

Entry
Database: PDB / ID: 5h94
TitleCrystal structure of Swine MHC CLASSI for 1.48 angstroms
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nonapeptide from Influenza A virus HA protein
KeywordsIMMUNE SYSTEM / Swine / Crystal structure / MHC I / Influenza A virus / Mechanism / CTL immunity
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 / viral budding from plasma membrane / 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 / viral budding from plasma membrane / 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 / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / immune response / apical plasma membrane / external side of plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular space / extracellular region
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Hemagglutinin / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
H1N1 swine influenza virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsFan, S. / Zhang, N. / Wang, S. / Wu, Y. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
The 863 Project of the China Ministry of Science and TechnologyNo. 2013AA102503 China
CitationJournal: J.Virol. / Year: 2016
Title: Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains
Authors: Fan, S. / Wu, Y. / Wang, S. / Wang, Z. / Jiang, B. / Liu, Y. / Liang, R. / Zhou, W. / Zhang, N. / Xia, C.
History
DepositionDec 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Nonapeptide from Influenza A virus HA protein
D: MHC class I antigen
E: Beta-2-microglobulin
F: Nonapeptide from Influenza A virus HA protein


Theoretical massNumber of molelcules
Total (without water)88,3326
Polymers88,3326
Non-polymers00
Water14,916828
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nonapeptide from Influenza A virus HA protein


Theoretical massNumber of molelcules
Total (without water)44,1663
Polymers44,1663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-18 kcal/mol
Surface area18610 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: Nonapeptide from Influenza A virus HA protein


Theoretical massNumber of molelcules
Total (without water)44,1663
Polymers44,1663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-17 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.453, 41.471, 106.735
Angle α, β, γ (deg.)90.00, 117.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31693.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-3*hs0202 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9JT91*PLUS
#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 Nonapeptide from Influenza A virus HA protein


Mass: 1040.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) H1N1 swine influenza virus / References: UniProt: C4RUF0*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE OF MHC CLASS I ANTIGEN USED IN THIS STRUCTURE HAS BEEN DEPOSITED TO DATABASE.

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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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20%(w/v) Polyethylene glycol 3350, 0.2M Ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2014
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 127299 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 19.482
Reflection shellResolution: 1.48→1.518 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.536 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data reduction
PHASERdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ4

3qq4


Resolution: 1.48→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.639 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19025 6668 5 %RANDOM
Rwork0.14975 ---
obs0.15177 127299 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å21.28 Å2
2---4.47 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 0 828 7048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0196432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9328746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91924.062352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.035151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3941546
X-RAY DIFFRACTIONr_chiral_restr0.170.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215117
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.2641.7883054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.962.7053807
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1072.143376
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.17117.1910727
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.27336430
X-RAY DIFFRACTIONr_sphericity_free28.645218
X-RAY DIFFRACTIONr_sphericity_bonded24.73356857
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 459 -
Rwork0.26 9089 -
obs--97.2 %

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