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- PDB-4prd: Crystal structure of a HLA-B*35:08-HPVG-D5 -

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Basic information

Entry
Database: PDB / ID: 4prd
TitleCrystal structure of a HLA-B*35:08-HPVG-D5
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Epstein-Barr nuclear antigen 1Epstein–Barr virus 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


symbiont-mediated suppression of host antigen processing and presentation / viral latency / : / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA replication / 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding ...symbiont-mediated suppression of host antigen processing and presentation / viral latency / : / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA replication / 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HLA-B*3507 / Beta-2-microglobulin / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1054
Polymers45,0463
Non-polymers591
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-17 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.900, 82.000, 110.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31984.281 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 / 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 / Epstein–Barr virus nuclear antigen 1 / EBNA-1 / EBV nuclear antigen 1


Mass: 1313.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KSS4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 51.9 %
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: Mar 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 47357 / Num. obs: 47357 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.95 Å2 / Rmerge(I) obs: 0.054 / Χ2: 0.964 / Net I/σ(I): 24.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.850.3146.4651872712499.7
1.85-1.950.2029.85427945802100
1.95-20.14613.21182982472100
2-2.20.10917.05578047819100
2.2-2.50.07523.58557037543100
2.5-30.05132.42505296880100
3-50.03347.93540257511100
5-60.03152.016262902100
6-100.03251.16683100499.9
100.03249.47166530097.4

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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: 1.75→46.224 Å / FOM work R set: 0.843 / SU ML: 0.49 / σ(F): 1.35 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 2398 5.06 %randomn
Rwork0.194 ---
obs0.196 47349 99.91 %-
all-47349 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.78 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 71.74 Å2 / Biso mean: 21.52 Å2 / Biso min: 2.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.7815 Å2-0 Å20 Å2
2---3.4355 Å2-0 Å2
3---6.217 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 4 421 3605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123395
X-RAY DIFFRACTIONf_angle_d1.1724627
X-RAY DIFFRACTIONf_chiral_restr0.101467
X-RAY DIFFRACTIONf_plane_restr0.005621
X-RAY DIFFRACTIONf_dihedral_angle_d14.0251274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.78570.35041520.28052581273399
1.7857-1.82460.32291510.260825812732100
1.8246-1.8670.28911280.237526222750100
1.867-1.91370.27011380.220825782716100
1.9137-1.96540.28471440.209626442788100
1.9654-2.02330.27411460.196325922738100
2.0233-2.08860.23071190.192826342753100
2.0886-2.16320.26431270.191226332760100
2.1632-2.24980.23711400.200826412781100
2.2498-2.35220.24611610.188825972758100
2.3522-2.47620.23761390.196426482787100
2.4762-2.63140.22511460.198526362782100
2.6314-2.83450.24011150.203326952810100
2.8345-3.11970.21731510.196326472798100
3.1197-3.5710.22921450.193126782823100
3.571-4.49850.18481340.154527132847100
4.4985-46.23980.21161620.187528312993100

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