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- PDB-3oxr: Crystal Structure of HLA A*02:06 Bound to HBV Core 18-27 -

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Basic information

Entry
Database: PDB / ID: 3oxr
TitleCrystal Structure of HLA A*02:06 Bound to HBV Core 18-27
Components
  • 10mer peptide from Pre-core-protein
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Protein-Peptide Complex / Host-virus interaction / Immunogenicity / Therapeutic Design / TCR Recognition / Helix / Beta-sheet / Antigen Presentation / Peptide Binding / Cell Surface
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / antigen processing and presentation / virus-mediated perturbation of host defense response / 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 ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / antigen processing and presentation / virus-mediated perturbation of host defense response / 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 / 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 / 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 / viral penetration into host nucleus / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / membrane => GO:0016020 / learning or memory / immune response / symbiont entry into host cell / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / 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 ...Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / 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
External core antigen / Beta-2-microglobulin / HLA class I histocompatibility antigen A alpha chain / External core antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, J. / Chen, Y. / Lai, L. / Ren, E.
CitationJournal: Eur.J.Immunol. / Year: 2011
Title: Structural insights into the binding of hepatitis B virus core peptide to HLA-A2 alleles: Towards designing better vaccines.
Authors: Liu, J. / Chen, K.Y. / Ren, E.C.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: 10mer peptide from Pre-core-protein


Theoretical massNumber of molelcules
Total (without water)44,9053
Polymers44,9053
Non-polymers00
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-23 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.400, 79.200, 60.200
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

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Components

#1: Protein MHC class I antigen / CLASS I HISTOCOMPATIBILITY ANTIGEN


Mass: 31870.203 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, MHC HLA-A*02:06 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5MAG5
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA 2-MICROGLOBULIN, CDABP0092, HDCMA22P / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide 10mer peptide from Pre-core-protein


Mass: 1155.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Hepatitis B Virus Core 18-27 is synthesized. / Source: (synth.) Hepatitis B virus / References: UniProt: Q9YJW5, UniProt: P0C6H2*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 10% w/v Polyethylene glycol 6,000, 5% v/v (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.67→59.78 Å / Num. all: 62992 / Num. obs: 62992 / % possible obs: 96.02 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.92
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.67-1.733.50.472.85871191.7
1.73-1.83.60.3493.85818194.5
1.8-1.883.60.2295.65653195
1.88-1.973.60.1478.65391195.3
1.97-2.083.60.09912.25153195.8
2.08-2.213.60.07415.84892196

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HHH

1hhh


Resolution: 1.7→59.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.922 / SU ML: 0.064 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21404 2808 5.1 %RANDOM
Rwork0.1772 ---
obs0.17911 52482 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 0 457 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9234430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8575382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39623.125176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69215526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5521528
X-RAY DIFFRACTIONr_chiral_restr0.1330.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212579
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.111.51920
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.47623097
X-RAY DIFFRACTIONr_scbond_it5.28631343
X-RAY DIFFRACTIONr_scangle_it8.1884.51333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 179 -
Rwork0.279 3808 -
obs--94.34 %

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