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- PDB-1zsd: Crystal Structure Of HLA-B*3501 Presenting an 11-Mer EBV Antigen ... -

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Basic information

Entry
Database: PDB / ID: 1zsd
TitleCrystal Structure Of HLA-B*3501 Presenting an 11-Mer EBV Antigen EPLPQGQLTAY
Components
  • BZLF1 trans-activator protein
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
KeywordsIMMUNE SYSTEM / Human leukocyte antigen / major histocompatibility complex I / B35 / B*3501 / bulged peptide
Function / homology
Function and homology information


symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / 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 ...symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / sequence-specific DNA binding / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / protein dimerization activity / immune response / endoplasmic reticulum lumen / DNA-binding transcription factor activity / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / DNA binding
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMiles, J.J. / Elhassen, D. / Borg, N.A. / Silins, S.L. / Tynan, F.E. / Burrows, J.M. / Purcell, A.W. / Kjer-Nielsen, L. / Rossjohn, J. / Burrows, S.R. / McCluskey, J.
CitationJournal: J.Immunol. / Year: 2005
Title: CTL Recognition of a Bulged Viral Peptide Involves Biased TCR Selection.
Authors: Miles, J.J. / Elhassen, D. / Borg, N.A. / Silins, S.L. / Tynan, F.E. / Burrows, J.M. / Purcell, A.W. / Kjer-Nielsen, L. / Rossjohn, J. / Burrows, S.R. / McCluskey, J. / El-Hassen, D.
History
DepositionMay 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 23, 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 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: BZLF1 trans-activator protein


Theoretical massNumber of molelcules
Total (without water)44,9053
Polymers44,9053
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-21 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.930, 81.490, 109.920
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-35 alpha chain / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: extracellular domains alpha-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / HDCMA22P


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: beta-2-microglobulin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide BZLF1 trans-activator protein / EB1 / Zebra


Mass: 1216.339 Da / Num. of mol.: 1 / Fragment: EBV peptide EPLPQGQLTAY / Source method: obtained synthetically / References: UniProt: P03206
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M ammonium acetate, 17% w/v PEG 3350, 100mM cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 47652 / % possible obs: 93.4 % / Rmerge(I) obs: 0.079 / Χ2: 1.242
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsΧ2
1.7-1.7675.80.66738151.204
1.76-1.8385.30.58742721.205
1.83-1.9190.30.42945651.296
1.91-2.0293.50.26846961.357
2.02-2.1495.10.19148371.419
2.14-2.3197.30.13349371.348
2.31-2.5499.30.09450471.232
2.54-2.9199.70.0750961.209
2.91-3.6699.70.04751581.16
3.66-10096.80.04152291.021

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A1N

1a1n


Resolution: 1.7→25.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.246 1926 3.8 %
Rwork0.219 --
obs0.219 47608 93.1 %
Solvent computationBsol: 46.32 Å2
Displacement parametersBiso mean: 21.858 Å2
Baniso -1Baniso -2Baniso -3
1-2.254 Å20 Å20 Å2
2--6.371 Å20 Å2
3----8.626 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 0 394 3560
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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