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- PDB-2bvp: Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identif... -

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Entry
Database: PDB / ID: 2bvp
TitleStructures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs Potentially Associated with Long-Term Non-Progression
Components
  • BETA-2-MICROGLOBULIN
  • HIV-P24
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN
KeywordsGLYCOPROTEIN/PEPTIDE / MHC / HLA-B57 / LTNP / HIV-1 / GLYCOPROTEIN / MHC I / POLYMORPHISM / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / GLYCOPROTEIN-PEPTIDE COMPLEX / IMMUNE RESPONSE
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / protection from natural killer cell mediated cytotoxicity / TAP binding / detection of bacterium / 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 / beta-2-microglobulin binding ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / protection from natural killer cell mediated cytotoxicity / TAP binding / detection of bacterium / 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 / beta-2-microglobulin binding / regulation of natural killer cell mediated immunity / early endosome lumen / positive regulation of T cell mediated cytotoxicity / secretory granule membrane / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / defense response / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / viral nucleocapsid / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / adaptive immune response / host cell cytoplasm / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / viral translational frameshifting / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / host cell nucleus / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 / MHC classes I/II-like antigen recognition protein / : / Retrovirus capsid, N-terminal / 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 class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Gag protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.35 Å
AuthorsStewart-Jones, G.B. / Gillespie, G. / Overton, I.M. / Kaul, R. / Roche, P. / Mcmichael, A.J. / Rowland-Jones, S. / Jones, E.Y.
CitationJournal: J Immunol. / Year: 2005
Title: Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression.
Authors: Stewart-Jones, G.B. / Gillespie, G. / Overton, I.M. / Kaul, R. / Roche, P. / McMichael, A.J. / Rowland-Jones, S. / Jones, E.Y.
History
DepositionJul 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 1.4Oct 9, 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 / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: HIV-P24


Theoretical massNumber of molelcules
Total (without water)44,7503
Polymers44,7503
Non-polymers00
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.912, 81.887, 108.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN / HLA-B5703 / MHC CLASS I ANTIGEN B*57 / BW-57


Mass: 31811.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGM-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGM-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide HIV-P24


Mass: 1059.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q8URG0*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 33.88 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.973
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 98052 / % possible obs: 98.1 % / Observed criterion σ(I): 0.9 / Redundancy: 9.5 % / Rmerge(I) obs: 0.06

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.35→65.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.038 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4806 5 %RANDOM
Rwork0.197 ---
obs0.198 91216 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.35→65.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 0 769 3897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9314373
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66623.121173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69215519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6581531
X-RAY DIFFRACTIONr_chiral_restr0.080.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21862
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22246
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2725
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7371.51939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2723074
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83131471
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8234.51299
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 308 -
Rwork0.3 6084 -
obs--89.09 %

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