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- PDB-3qq4: Crystal structure of swine major histocompatibility complex class... -

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Basic information

Entry
Database: PDB / ID: 3qq4
TitleCrystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • VP35
KeywordsIMMUNE SYSTEM / Swine MHC Class 1 / SLA-1*0401 / Epitope of Ebola virus
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / virion component => GO:0044423 / Neutrophil degranulation ...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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / virion component => GO:0044423 / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / MHC class II protein complex binding / late endosome membrane / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / immune response / lysosomal membrane / extracellular region / cytoplasm
Similarity search - Function
Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / 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 ...Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / 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
Polymerase cofactor VP35 / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
Sudan ebolavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsZhang, N. / Qi, J. / Gao, F. / Pan, X. / Chen, R. / Li, Q. / Chen, Z. / Li, X. / Xia, C. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2011
Title: Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides.
Authors: Zhang, N. / Qi, J. / Feng, S. / Gao, F. / Liu, J. / Pan, X. / Chen, R. / Li, Q. / Chen, Z. / Li, X. / Xia, C. / Gao, G.F.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: VP35


Theoretical massNumber of molelcules
Total (without water)44,2583
Polymers44,2583
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-14 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.680, 40.238, 103.633
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen / SLA-1*0401-S-OIVAY9 Heavy Chain


Mass: 31681.988 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: PD1, SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O19244
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / SLA-1*0401-S-OIVAY9 Light Chain / Lactollin


Mass: 11708.207 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 VP35 / Peptide of SLA-1*0401-S-OIVAY9


Mass: 867.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Sudan ebolavirus / References: UniProt: C4PK56
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% v/v Jeffamine M-600 pH7.0, 0.1M BIS-TRIS pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.097→50 Å / Num. all: 21639 / Num. obs: 21639 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q94

1q94


Resolution: 2.097→23.823 Å / SU ML: 0.28 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1109 5.13 %RANDOM
Rwork0.1923 ---
all0.1946 21634 --
obs0.1946 21634 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.47 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8552 Å20 Å2-2.5719 Å2
2---4.9425 Å20 Å2
3---0.188 Å2
Refinement stepCycle: LAST / Resolution: 2.097→23.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 0 330 3436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033191
X-RAY DIFFRACTIONf_angle_d0.7634333
X-RAY DIFFRACTIONf_dihedral_angle_d17.1131152
X-RAY DIFFRACTIONf_chiral_restr0.056443
X-RAY DIFFRACTIONf_plane_restr0.003573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0974-2.19280.28411380.1917245897
2.1928-2.30840.26531150.2016255099
2.3084-2.45290.2971330.2117256199
2.4529-2.6420.2331200.2074255199
2.642-2.90750.25191490.21362577100
2.9075-3.32720.2331210.19492596100
3.3272-4.18820.21911680.17322572100
4.1882-23.82410.19881650.17342660100

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