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- PDB-5hga: HLA*A2402 complex with HIV nef138 Y2F-8mer mutant epitope -

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Basic information

Entry
Database: PDB / ID: 5hga
TitleHLA*A2402 complex with HIV nef138 Y2F-8mer mutant epitope
Components
  • 8-mer from Protein Nef
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
KeywordsIMMUNE SYSTEM / HLA / Antigen presentation / HIV
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target ...Nef mediated downregulation of CD28 cell surface expression / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Uncoating of the HIV Virion / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / host cell Golgi membrane / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Binding and entry of HIV virion / detection of bacterium / T cell 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / Assembly Of The HIV Virion / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Budding and maturation of HIV virion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / SH3 domain binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / virion component / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 ...HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Protein Nef / HLA class I histocompatibility antigen, A alpha chain / Protein Nef / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsShi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Cell Rep / Year: 2016
Title: Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation.
Authors: Sun, X. / Shi, Y. / Akahoshi, T. / Fujiwara, M. / Gatanaga, H. / Schonbach, C. / Kuse, N. / Appay, V. / Gao, G.F. / Oka, S. / Takiguchi, M.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-24 alpha chain
B: Beta-2-microglobulin
C: 8-mer from Protein Nef
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: 8-mer from Protein Nef


Theoretical massNumber of molelcules
Total (without water)89,1736
Polymers89,1736
Non-polymers00
Water2,774154
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: 8-mer from Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,5873
Polymers44,5873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area18430 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: 8-mer from Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,5873
Polymers44,5873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-24 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.838, 86.913, 151.441
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, A-24 alpha chain / Aw-24 / HLA class I histocompatibility antigen / A-9 alpha chain / MHC class I antigen A*24


Mass: 31683.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P61769
#3: Protein/peptide 8-mer from Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 1024.195 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 135-142 / Mutation: Y2F / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P18801, UniProt: P04601*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 0.1M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 324304 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 24.39
Reflection shellResolution: 2.199→2.28 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.588 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.199→37.86 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 2225 5.03 %
Rwork0.2053 --
obs0.2075 44202 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.199→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 0 154 6416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066442
X-RAY DIFFRACTIONf_angle_d1.0558720
X-RAY DIFFRACTIONf_dihedral_angle_d16.6272376
X-RAY DIFFRACTIONf_chiral_restr0.075882
X-RAY DIFFRACTIONf_plane_restr0.0051146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1991-2.24690.30161360.27492539X-RAY DIFFRACTION98
2.2469-2.29920.33441640.26542592X-RAY DIFFRACTION100
2.2992-2.35670.31071470.26112558X-RAY DIFFRACTION100
2.3567-2.42040.31481480.25572588X-RAY DIFFRACTION100
2.4204-2.49160.33581510.2522571X-RAY DIFFRACTION100
2.4916-2.5720.32131200.2512601X-RAY DIFFRACTION100
2.572-2.66390.31341520.2422585X-RAY DIFFRACTION100
2.6639-2.77050.31481320.24582611X-RAY DIFFRACTION100
2.7705-2.89660.31061280.24262618X-RAY DIFFRACTION100
2.8966-3.04920.27741490.24332600X-RAY DIFFRACTION100
3.0492-3.24020.27561300.22082639X-RAY DIFFRACTION100
3.2402-3.49020.28421180.22112647X-RAY DIFFRACTION100
3.4902-3.84110.22951390.2012649X-RAY DIFFRACTION100
3.8411-4.39620.20661250.17472669X-RAY DIFFRACTION100
4.3962-5.5360.17951490.15742683X-RAY DIFFRACTION100
5.536-37.86580.22091370.17892827X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.0244 Å / Origin y: 0.6499 Å / Origin z: -18.2876 Å
111213212223313233
T0.1439 Å20.0343 Å2-0.0199 Å2-0.1263 Å20.0178 Å2--0.1442 Å2
L0.1676 °20.1446 °2-0.1407 °2-0.008 °20.1693 °2--0.2338 °2
S0.036 Å °-0.0219 Å °0.0388 Å °-0.0346 Å °-0.0406 Å °-0.0098 Å °-0.0267 Å °0.0198 Å °-0.0155 Å °
Refinement TLS groupSelection details: all

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