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- PDB-3vxn: HLA-A24 in complex with HIV-1 Nef134-10(wt) -

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Basic information

Entry
Database: PDB / ID: 3vxn
TitleHLA-A24 in complex with HIV-1 Nef134-10(wt)
Components
  • 10-mer peptide from Protein Nef
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
KeywordsIMMUNE SYSTEM / HIV-1 / NEF / HLA-A24 / MHC CLASS I / IMMUNOGLOBURIN DOMAIN / MHC / IMMUNE ESPONSE
Function / homology
Function and homology information


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 / 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 ...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 / 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 / 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 / host cell Golgi membrane / 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 / 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 / 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 / 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 / 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 / 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 / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma 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 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Protein Nef
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShimizu, A. / Fukai, S. / Yamagata, A. / Iwamoto, A.
CitationJournal: SCI REP / Year: 2013
Title: Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. ...Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. / Fukai, S. / Iwamoto, A.
History
DepositionSep 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: 10-mer peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,8533
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-20 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.069, 65.029, 50.057
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number5
Space group name H-MC121

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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 / Plasmid: PET21D(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide 10-mer peptide from Protein Nef


Mass: 1290.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YYU8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5% PEG 8000, 50mM ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 35709 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.199 / Num. unique all: 1612 / % possible all: 84.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I6L

3i6l


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.353 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1793 5 %RANDOM
Rwork0.1693 ---
obs0.1732 35708 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.647 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20.23 Å2
2--0.85 Å2-0 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 0 204 3347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.934386
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79523.2175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07615528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2211529
X-RAY DIFFRACTIONr_chiral_restr0.0980.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr5.37733233
X-RAY DIFFRACTIONr_sphericity_free26.283563
X-RAY DIFFRACTIONr_sphericity_bonded15.3953284
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 102 -
Rwork0.251 2131 -
obs--80.32 %

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