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

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Basic information

Entry
Database: PDB / ID: 2bvq
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-PEPTIDE COMPLEX / MHC I / POLYMORPHISM / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / 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 / MHC class Ib protein complex / viral process / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...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 / MHC class Ib protein complex / viral process / 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 / positive regulation of T cell mediated cytotoxicity / early endosome lumen / 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 / defense response / 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 / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / specific granule lumen / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / tertiary granule lumen / Modulation by Mtb of host immune system / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / lysosomal membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 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: 2 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 1.4Nov 13, 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)44,9573
Polymers44,9573
Non-polymers00
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.810, 82.640, 110.650
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 / MHC CLASS I ANTIGEN B*57 / BW-57 / HLA-B5703


Mass: 31811.285 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-300
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 / Fragment: RESIDUES 21-119
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: 1266.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q70A61*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.43 Å3/Da / Density % sol: 48.94 %

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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: 2→30 Å / Num. obs: 32321 / % possible obs: 99.3 % / Observed criterion σ(I): 0.9 / Redundancy: 8 % / Rmerge(I) obs: 0.01

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2→66.23 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.523 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1618 5.1 %RANDOM
Rwork0.204 ---
obs0.208 30389 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---1 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 2→66.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 0 297 3416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0213208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9344359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33923.198172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85115519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5951530
X-RAY DIFFRACTIONr_chiral_restr0.170.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21108
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22025
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3351.52008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98223072
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.23931469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8044.51287
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 86 -
Rwork0.238 2103 -
obs--92.56 %

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