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- PDB-2axf: The Immunogenicity of a Viral Cytotoxic T Cell Epitope is control... -

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Basic information

Entry
Database: PDB / ID: 2axf
TitleThe Immunogenicity of a Viral Cytotoxic T Cell Epitope is controlled by its MHC-bound Conformation
Components
  • 10-mer peptide from BZLF1 trans-activator protein
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B*3508 heavy chain
KeywordsIMMUNE SYSTEM/GENE REGULATION / immune response / pMHC / IMMUNE SYSTEM-GENE REGULATION COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / sequence-specific DNA binding / adaptive immune response / learning or memory / protein dimerization activity / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus / chromatin / Neutrophil degranulation / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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
ACETIC ACID / HLA class I histocompatibility antigen, B alpha chain / Lytic switch protein BZLF1 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTynan, F.E. / Elhassen, D. / Purcell, A.W. / Burrows, J.M. / Borg, N.A. / Miles, J.J. / Williamson, N.A. / Green, K.J. / Tellam, J. / Kjer-Nielsen, L. ...Tynan, F.E. / Elhassen, D. / Purcell, A.W. / Burrows, J.M. / Borg, N.A. / Miles, J.J. / Williamson, N.A. / Green, K.J. / Tellam, J. / Kjer-Nielsen, L. / McCluskey, J. / Rossjohn, J. / Burrows, S.R.
CitationJournal: J.Exp.Med. / Year: 2005
Title: The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation
Authors: Tynan, F.E. / Elhassen, D. / Purcell, A.W. / Burrows, J.M. / Borg, N.A. / Miles, J.J. / Williamson, N.A. / Green, K.J. / Tellam, J. / Kjer-Nielsen, L. / McCluskey, J. / Rossjohn, J. / Burrows, S.R.
History
DepositionSep 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B*3508 heavy chain
B: Beta-2-microglobulin
C: 10-mer peptide from BZLF1 trans-activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9105
Polymers44,7903
Non-polymers1202
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-18 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.825, 81.528, 110.732
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 HLA class I histocompatibility antigen, B*3508 heavy chain / HLA-B*3508 Class I histocompatibility antigen / MHC class I antigen B*3508


Mass: 31984.281 Da / Num. of mol.: 1 / Fragment: residues 1-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide 10-mer peptide from BZLF1 trans-activator protein / EBV / EB1 / Zebra


Mass: 1057.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide APQPAPENAY / References: UniProt: P03206
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 200mM Ammonium Acetate, 17% W/V PEG 3350, 100mM Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 43444 / Num. obs: 43173 / Redundancy: 3.7 %
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.83

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2339 2167 random
Rwork0.2082 --
obs0.209 40906 -
all-43073 -
Displacement parametersBiso mean: 30.6224 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 0 524 3707

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