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- PDB-4k7f: Newly identified epitope V60 from HBV core protein complexed with... -

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Basic information

Entry
Database: PDB / ID: 4k7f
TitleNewly identified epitope V60 from HBV core protein complexed with HLA-A*0201
Components
  • Beta-2-microglobulin
  • Core protein
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / Host-virus interaction / immune response / Disease mutation / viral replication / Ig-like domain / TCR / membrane glycoprotein / viral capsid protein
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / viral penetration into host nucleus / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / host cell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / symbiont entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation
Similarity search - Function
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 ...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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Capsid protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMeng, S.D. / Zhang, Y. / Wu, Y. / Qi, J.X.
CitationJournal: J.Virol. / Year: 2013
Title: The L60V variation in hepatitis B virus core protein elicits new epitope-specific cytotoxic T lymphocytes and enhances viral replication.
Authors: Zhang, Y. / Ren, Y. / Wu, Y. / Zhao, B. / Qiu, L. / Li, X. / Xu, D. / Liu, J. / Gao, G.F. / Meng, S.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Core protein
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Core protein


Theoretical massNumber of molelcules
Total (without water)89,5966
Polymers89,5966
Non-polymers00
Water22,4291245
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Core protein


Theoretical massNumber of molelcules
Total (without water)44,7983
Polymers44,7983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-27 kcal/mol
Surface area18840 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Core protein


Theoretical massNumber of molelcules
Total (without water)44,7983
Polymers44,7983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-27 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.864, 58.552, 89.581
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Core protein


Mass: 1064.278 Da / Num. of mol.: 2 / Fragment: UNP residues 60-68 / Source method: obtained synthetically
Details: This sequence occurs naturally in hepatitis B virus
Source: (synth.) Hepatitis B virus / References: UniProt: Q9QAC5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1245 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 20%(wt/vol) polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 54699 / Num. obs: 54383 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 15.24 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.856 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8079 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 2753 5.06 %
Rwork0.2043 51625 -
obs0.207 54378 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.35 Å2 / Biso mean: 22.3947 Å2 / Biso min: 3.81 Å2
Refinement stepCycle: LAST / Resolution: 2→29.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 0 1245 7555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036521
X-RAY DIFFRACTIONf_angle_d0.6888848
X-RAY DIFFRACTIONf_chiral_restr0.052903
X-RAY DIFFRACTIONf_plane_restr0.0031155
X-RAY DIFFRACTIONf_dihedral_angle_d14.0092386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03450.32991300.24042342247290
2.0345-2.07150.29711210.23332402252392
2.0715-2.11130.31320.2252446257894
2.1113-2.15440.27971240.20712472259694
2.1544-2.20120.27591340.21692527266197
2.2012-2.25240.29971250.21312588271398
2.2524-2.30870.25131330.22012551268498
2.3087-2.37110.30011390.22232613275298
2.3711-2.44090.30061270.22272629275699
2.4409-2.51960.34041310.216625982729100
2.5196-2.60960.261540.227126072761100
2.6096-2.7140.29591400.219526072747100
2.714-2.83740.27371540.227926322786100
2.8374-2.98690.27151410.215526472788100
2.9869-3.17390.27441580.21325832741100
3.1739-3.41860.25721580.194626632821100
3.4186-3.7620.25661280.17826382766100
3.762-4.3050.19191610.171226452806100
4.305-5.41860.20711300.168426762806100
5.4186-29.85910.21631330.208227592892100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16390.1003-0.07161.21360.030.1868-0.00780.0069-0.0271-0.10740.014-0.2604-0.0293-0.0067-0.00180.04410.00810.01310.07820.01220.09496.80671.924437.1271
20.7267-0.21220.01371.3356-0.02850.6170.0098-0.129-0.12930.24890.0967-0.08620.01320.1149-0.0250.0880.0172-0.03970.0864-0.00330.06964.1807-8.246953.157
30.0845-0.15710.03441.10540.09770.22720.00210.0120.03340.0880.0021-0.08130.0472-0.00940.00240.051-0.0029-0.01570.08650.0070.037221.7014.91884.8325
40.7941-0.0588-0.08071.19990.17040.88370.05710.02760.0804-0.1288-0.0517-0.1144-0.01730.0136-0.0040.05540.00380.00260.0616-0.00360.073219.516314.9989-11.3126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 2:275)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 0:99)
3X-RAY DIFFRACTION3(CHAIN D AND RESSEQ 1:275)
4X-RAY DIFFRACTION4(CHAIN E AND RESSEQ 0:99)

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