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- PDB-3pwv: An immmunodominant CTL epitope from rinderpest virus presented by... -

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Basic information

Entry
Database: PDB / ID: 3pwv
TitleAn immmunodominant CTL epitope from rinderpest virus presented by cattle MHC class I molecule N*01801 (BoLA-A11)
Components
  • 9-mer peptide from Hemagglutinin
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC BoLA-A11 conformation cattle / immunodominant epitope
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / host cell membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / host cell membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / host cell surface receptor binding / immune response / lysosomal membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
: / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-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 ...: / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen / Hemagglutinin glycoprotein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Rinderpest virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.696 Å
AuthorsLi, X. / Liu, J. / Qi, J. / Gao, F. / Li, Q. / Li, X. / Zhang, N. / Xia, C. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2011
Title: Two distinct conformations of a rinderpest virus epitope presented by bovine major histocompatibility complex class I N*01801: a host strategy to present featured peptides
Authors: Li, X. / Liu, J. / Qi, J. / Gao, F. / Li, Q. / Li, X. / Zhang, N. / Xia, C. / Gao, G.F.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 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: 9-mer peptide from Hemagglutinin
D: MHC class I antigen
E: Beta-2-microglobulin
F: 9-mer peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)88,7936
Polymers88,7936
Non-polymers00
Water2,072115
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: 9-mer peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)44,3963
Polymers44,3963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-23 kcal/mol
Surface area19070 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: 9-mer peptide from Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)44,3963
Polymers44,3963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-21 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.905, 83.905, 153.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein MHC class I antigen


Mass: 31797.080 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LA-A11 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95477
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11653.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: B2M / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01888
#3: Protein/peptide 9-mer peptide from Hemagglutinin


Mass: 946.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized artificially / Source: (synth.) Rinderpest virus / References: UniProt: Q9YKD7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 18, 2010
RadiationMonochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.696→50 Å / Num. obs: 28833 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 16.186
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 4.302 / Rsym value: 0.548 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+27 / Resolution: 2.696→30.225 Å / SU ML: 0.33 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1441 5.07 %none
Rwork0.1882 ---
obs0.1905 28440 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.776 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8527 Å20 Å2-0 Å2
2--1.8527 Å20 Å2
3----3.7053 Å2
Refinement stepCycle: LAST / Resolution: 2.696→30.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 115 6381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066450
X-RAY DIFFRACTIONf_angle_d0.8928752
X-RAY DIFFRACTIONf_dihedral_angle_d18.8822362
X-RAY DIFFRACTIONf_chiral_restr0.064884
X-RAY DIFFRACTIONf_plane_restr0.0041162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6955-2.79180.29061200.2265254792
2.7918-2.90350.29141670.217259395
2.9035-3.03550.24821360.2229266396
3.0355-3.19540.28781400.2179265697
3.1954-3.39540.25211340.206274398
3.3954-3.65710.23911480.1815272999
3.6571-4.02440.2071500.16962748100
4.0244-4.6050.17971480.15482774100
4.605-5.79510.20431570.15422743100
5.7951-30.22640.20571410.1825280399
Refinement TLS params.Method: refined / Origin x: 11.1723 Å / Origin y: -43.9447 Å / Origin z: -11.2455 Å
111213212223313233
T0.1739 Å20.0101 Å2-0.0148 Å2-0.0886 Å20.0182 Å2--0.1277 Å2
L0.0892 °20.1056 °20.1362 °2-0.3104 °20.1698 °2--0.2035 °2
S0.0395 Å °-0.0008 Å °-0.0473 Å °-0.0235 Å °0.0018 Å °-0.0097 Å °0.0952 Å °-0.007 Å °-0.0411 Å °
Refinement TLS groupSelection details: all

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