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- PDB-3qq3: Crystal structure of swine major histocompatibility complex class... -

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Basic information

Entry
Database: PDB / ID: 3qq3
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
  • 9-mer peptide from Neuraminidase
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Swine MHC Class 1 / SLA-1*0401 / Epitope of Influenza 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 / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / : / : ...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 / : / : / : / exo-alpha-sialidase / viral budding from plasma membrane / 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 / MHC class II protein complex binding / late endosome membrane / carbohydrate metabolic process / immune response / lysosomal membrane / host cell plasma membrane / virion membrane / extracellular region / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / 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 ...Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / 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 / Beta-2-microglobulin / Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesSus scrofa (pig)
Influenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 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

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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: 9-mer peptide from Neuraminidase
D: MHC class I antigen
E: Beta-2-microglobulin
F: 9-mer peptide from Neuraminidase


Theoretical massNumber of molelcules
Total (without water)88,8836
Polymers88,8836
Non-polymers00
Water6,179343
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: 9-mer peptide from Neuraminidase


Theoretical massNumber of molelcules
Total (without water)44,4413
Polymers44,4413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-15 kcal/mol
Surface area19000 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: 9-mer peptide from Neuraminidase


Theoretical massNumber of molelcules
Total (without water)44,4413
Polymers44,4413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-15 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.731, 37.651, 111.430
Angle α, β, γ (deg.)90.00, 113.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen / SLA-1*0401-S-OIVNW9 Heavy Chain


Mass: 31681.988 Da / Num. of mol.: 2 / 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 / SLA-1*0401-S-OIVNW9 Light Chain / Lactollin


Mass: 11708.207 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 9-mer peptide from Neuraminidase / Peptide of SLA-1*0401-S-OIVNW9


Mass: 1051.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Influenza A virus / References: UniProt: Q9WDF0, UniProt: Q9Q0U7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% w/v polyethylene glycol 3350, 0.1M BIS-TRIS pH 6.5, 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 25, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 26179 / Num. obs: 26179 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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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 / Resolution: 2.59→28.312 Å / SU ML: 0.36 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1213 5.15 %RANDOM
Rwork0.1999 ---
obs0.203 23574 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.819 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3417 Å20 Å2-1.3004 Å2
2--0.1629 Å2-0 Å2
3----0.5046 Å2
Refinement stepCycle: LAST / Resolution: 2.59→28.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 0 343 6593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056434
X-RAY DIFFRACTIONf_angle_d0.8028738
X-RAY DIFFRACTIONf_dihedral_angle_d17.2072328
X-RAY DIFFRACTIONf_chiral_restr0.056884
X-RAY DIFFRACTIONf_plane_restr0.0031156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5902-2.69380.34711220.2753246299
2.6938-2.81630.35421340.24942417100
2.8163-2.96460.32341220.22982469100
2.9646-3.15020.29931420.21712490100
3.1502-3.3930.25391360.20082459100
3.393-3.73380.26321280.18162496100
3.7338-4.27250.21491370.16352476100
4.2725-5.37690.18171280.152537100
5.3769-28.31410.23161640.1773255599

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