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- PDB-5hgh: HLA*A2402 complexed with HIV nef138 10mer epitope -

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Basic information

Entry
Database: PDB / ID: 5hgh
TitleHLA*A2402 complexed with HIV nef138 10mer epitope
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • Protein Nef
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 / Uncoating of the HIV Virion / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / host cell Golgi membrane / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / Assembly Of The HIV Virion / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / Budding and maturation of HIV virion / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / SH3 domain binding / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / virion component / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane
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 / MOLECULAR REPLACEMENT / Resolution: 2.392 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: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,8533
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-25 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.735, 65.062, 50.415
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-444-

HOH

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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.: 1 / 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)
References: UniProt: P05534, UniProt: P04439*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) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#3: Protein/peptide Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 1290.511 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 135-144 / 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.: 238 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.392→50 Å / Num. obs: 20191 / % possible obs: 97.2 % / Redundancy: 4.1 % / Net I/σ(I): 19.968
Reflection shellResolution: 2.392→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.642 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.392→42.706 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 1048 5.17 %
Rwork0.1882 --
obs0.1901 19154 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.01 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.582 Å20 Å2-3.6086 Å2
2--10.365 Å20 Å2
3----0.7829 Å2
Refinement stepCycle: LAST / Resolution: 2.392→42.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 0 238 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033239
X-RAY DIFFRACTIONf_angle_d0.6894384
X-RAY DIFFRACTIONf_dihedral_angle_d17.4161173
X-RAY DIFFRACTIONf_chiral_restr0.047443
X-RAY DIFFRACTIONf_plane_restr0.002575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3919-2.5180.30771460.24432648X-RAY DIFFRACTION95
2.518-2.67580.29661420.23792684X-RAY DIFFRACTION97
2.6758-2.88230.27321450.21842739X-RAY DIFFRACTION97
2.8823-3.17230.24931530.2042767X-RAY DIFFRACTION98
3.1723-3.63110.22031470.17962754X-RAY DIFFRACTION98
3.6311-4.5740.17761540.14792809X-RAY DIFFRACTION99
4.574-42.71260.19141610.17612835X-RAY DIFFRACTION99

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