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- PDB-4pra: Crystal structure of a HLA-B*35:01-HPVG-Q5 -

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Basic information

Entry
Database: PDB / ID: 4pra
TitleCrystal structure of a HLA-B*35:01-HPVG-Q5
Components
  • Beta-2-microglobulin
  • Epstein-Barr nuclear antigen 1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / human leukocyte antigen class I / Epstein-Barr virus / viral escape / T cell receptor / viral immunity
Function / homology
Function and homology information


host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / antigen processing and presentation of peptide antigen via MHC class I / enzyme-substrate adaptor activity / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / antigen processing and presentation of peptide antigen via MHC class I / enzyme-substrate adaptor activity / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / MHC class II protein complex / 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 / 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 / peptide antigen binding / positive regulation of T cell activation / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / 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 / 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 / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / endonuclease activity / protein homotetramerization / amyloid fibril formation / symbiont-mediated suppression of host NF-kappaB cascade / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / DNA-binding transcription factor activity / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / 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 / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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-B*3507 / Epstein-Barr nuclear antigen 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsYu Chih, L. / Rossjohn, J. / Gras, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism.
Authors: Liu, Y.C. / Chen, Z. / Neller, M.A. / Miles, J.J. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Gras, S.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Jul 2, 2014Group: Database references
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 1


Theoretical massNumber of molelcules
Total (without water)45,0153
Polymers45,0153
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-19 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 81.430, 109.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein MHC class I antigen / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 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) / Strain (production host): BL21(DE3) / References: UniProt: C5MK56
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide Epstein-Barr nuclear antigen 1 / EBNA-1 / EBV nuclear antigen 1


Mass: 1326.389 Da / Num. of mol.: 1 / Fragment: unp residues 407-417 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: P03211
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGLU5 TO GLN5 IS A NATURAL VARIATION BETWEEN EBV STRAINS GLU5 IS FOUND IN EBV INFECTING CAUCASIAN ...GLU5 TO GLN5 IS A NATURAL VARIATION BETWEEN EBV STRAINS GLU5 IS FOUND IN EBV INFECTING CAUCASIAN GLN5 IS FOUND IN TYPE 1 EBV ISOLATES

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 16% PEG 4000, 0.2M ammonium acetate and 0.1M Na-Citrate, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 39526 / Num. obs: 39526 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.26 Å2 / Rmerge(I) obs: 0.076 / Χ2: 0.934 / Net I/σ(I): 21.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.950.4275.1542022570199.9
1.95-20.3017.2117848240899.9
2-2.50.17112.1311166315111100
2.5-30.08123.04497786754100
3-50.03447.37536087389100
5-60.02854.586180880100
6-100.02955.17665599099.9
100.02561.56165729397

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.14data extraction
Blu-Iceicedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FYY

2fyy


Resolution: 1.85→45.458 Å / FOM work R set: 0.8514 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1981 5.01 %
Rwork0.1899 --
all-39516 -
obs-39516 99.94 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.034 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 67.7 Å2 / Biso mean: 21.61 Å2 / Biso min: 5.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.3464 Å20 Å20 Å2
2---3.7223 Å20 Å2
3---6.0688 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 0 418 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083305
X-RAY DIFFRACTIONf_angle_d1.0744492
X-RAY DIFFRACTIONf_chiral_restr0.077455
X-RAY DIFFRACTIONf_plane_restr0.004597
X-RAY DIFFRACTIONf_dihedral_angle_d14.8031228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.89630.29221440.235826462790
1.8963-1.94750.26181320.209226502782
1.9475-2.00480.25811490.199826222771
2.0048-2.06960.24241590.194626142773
2.0696-2.14350.25981290.20126732802
2.1435-2.22930.2561400.194526432783
2.2293-2.33080.22881430.194526612804
2.3308-2.45370.25861400.199826492789
2.4537-2.60740.23531360.200626722808
2.6074-2.80870.24131450.205626892834
2.8087-3.09130.26461300.194626962826
3.0913-3.53850.19011280.191827322860
3.5385-4.45750.16451440.154727312875
4.4575-45.47160.20621620.181328573019

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