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- PDB-2hjk: Crystal Structure of HLA-B5703 and HIV-1 peptide -

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Basic information

Entry
Database: PDB / ID: 2hjk
TitleCrystal Structure of HLA-B5703 and HIV-1 peptide
Components
  • Beta-2-microglobulin
  • Gag protein
  • HLA class I histocompatibility antigen B-57
KeywordsIMMUNE SYSTEM / B57 / HLA / HIV
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / 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 ...viral budding via host ESCRT complex / viral process / 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 / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / 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 / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / immune response / viral translational frameshifting / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / virion membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / MHC classes I/II-like antigen recognition protein / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / : / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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
Beta-2-microglobulin / Gag polyprotein / GAG protein / HLA class I histocompatibility antigen B-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGillespie, G.M.A. / Stewart-Jones, G. / Rengasamy, J. / Beattie, T. / Bwayo, J.J. / Plummer, F.A.
CitationJournal: J.Immunol. / Year: 2006
Title: Strong TCR Conservation and Altered T Cell Cross-Reactivity Characterize a B*57-Restricted Immune Response in HIV-1 Infection.
Authors: Gillespie, G.M.A. / Stewart-Jones, G. / Rengasamy, J. / Beattie, T. / Bwayo, J.J. / Plummer, F.A. / Kaul, R. / McMichael, A.J. / Easterbrook, P. / Dong, T. / Jones, E.Y. / Rowland-Jones, S.L.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen B-57
B: Beta-2-microglobulin
C: Gag protein


Theoretical massNumber of molelcules
Total (without water)44,5503
Polymers44,5503
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-20 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.508, 81.553, 109.781
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 HLA class I histocompatibility antigen B-57 / MHC class I antigen


Mass: 31521.998 Da / Num. of mol.: 1 / Fragment: Residues 25-298 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9MYI6
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: Beta-2-microglobulin domain (Residues 21-119) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61769
#3: Protein/peptide Gag protein


Mass: 1279.525 Da / Num. of mol.: 1 / Fragment: Residues 160-170 / Source method: obtained synthetically / Details: Chemically synthesized. Occurs naturally in HIV 1 / References: UniProt: Q1M075, UniProt: Q70AA1*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→65.51 Å / Num. obs: 39498 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 1.85→1.92 Å / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→65.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.988 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1969 5 %RANDOM
Rwork0.193 ---
all-39498 --
obs-39240 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 0 343 3484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213231
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9364389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2323.237173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59715524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7821530
X-RAY DIFFRACTIONr_chiral_restr0.110.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022557
X-RAY DIFFRACTIONr_nbd_refined0.2380.21449
X-RAY DIFFRACTIONr_nbtor_refined0.310.22171
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2300
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.225
X-RAY DIFFRACTIONr_mcbond_it1.1571.51971
X-RAY DIFFRACTIONr_mcangle_it1.84423097
X-RAY DIFFRACTIONr_scbond_it2.83531466
X-RAY DIFFRACTIONr_scangle_it4.3344.51292
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 135 -
Rwork0.244 2629 -
obs-2764 97.43 %

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