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

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Basic information

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


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation / host cell membrane / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation / host cell membrane / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / membrane => GO:0016020 / learning or memory / host cell surface receptor binding / defense response to Gram-positive bacterium / immune response / symbiont entry into host cell / lysosomal membrane / external side of plasma membrane / innate immune response / viral envelope / virion attachment to host cell / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol
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 / Beta-2-Microglobulin ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / Hemagglutinin glycoprotein / MHC class I antigen
Similarity search - Component
Biological speciesBos taurus (cattle)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 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

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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: IPA from Hemagglutinin glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,4483
Polymers44,4483
Non-polymers00
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-22 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.913, 72.044, 120.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen / MHC class I N*01801


Mass: 31797.080 Da / Num. of mol.: 1 / Fragment: residues in UNP 26-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (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 / Beta-2 microglobulin / beta2m


Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: murine beta2m
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide IPA from Hemagglutinin glycoprotein


Mass: 946.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized artificially / References: UniProt: P41355
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 28, 2010
RadiationMonochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 32536 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.174
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.138 / Num. unique all: 2466 / Rsym value: 0.535 / % possible all: 100

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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: 1.899→23.956 Å / SU ML: 0.25 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 1645 5.06 %
Rwork0.1921 --
obs0.1941 32536 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.121 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0026 Å2-0 Å20 Å2
2---5.9462 Å2-0 Å2
3---0.9436 Å2
Refinement stepCycle: LAST / Resolution: 1.899→23.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 0 430 3562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053224
X-RAY DIFFRACTIONf_angle_d0.9094377
X-RAY DIFFRACTIONf_dihedral_angle_d19.241179
X-RAY DIFFRACTIONf_chiral_restr0.064446
X-RAY DIFFRACTIONf_plane_restr0.004580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8992-1.9550.29371180.22862348X-RAY DIFFRACTION89
1.955-2.01810.23471210.21442457X-RAY DIFFRACTION94
2.0181-2.09020.27591190.19972521X-RAY DIFFRACTION95
2.0902-2.17380.23951330.20312519X-RAY DIFFRACTION95
2.1738-2.27270.26551260.19492534X-RAY DIFFRACTION96
2.2727-2.39240.25211500.20112539X-RAY DIFFRACTION97
2.3924-2.54210.24881320.20632590X-RAY DIFFRACTION98
2.5421-2.73810.28331370.20862582X-RAY DIFFRACTION98
2.7381-3.01320.24221400.20052663X-RAY DIFFRACTION99
3.0132-3.44810.22331370.18732677X-RAY DIFFRACTION99
3.4481-4.34010.18371660.1672678X-RAY DIFFRACTION99
4.3401-23.95840.20141660.17182783X-RAY DIFFRACTION98

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