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- PDB-4u1k: HLA class I micropolymorphisms determine peptide-HLA landscape an... -

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Basic information

Entry
Database: PDB / ID: 4u1k
TitleHLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • Protein Nef
KeywordsIMMUNE SYSTEM / Immunoglobulin / HLA / HIV
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 / suppression by virus of host autophagy / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / activation of transmembrane receptor protein tyrosine kinase activity / regulation of interleukin-6 production / host cell Golgi membrane / host cell membrane ...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 / suppression by virus of host autophagy / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / activation of transmembrane receptor protein tyrosine kinase activity / regulation of interleukin-6 production / host cell Golgi membrane / host cell membrane / 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 / detection of bacterium / secretory granule membrane / virus-mediated perturbation of host defense response / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / endocytosis involved in viral entry into host cell / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / Golgi apparatus / cell surface
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Protein Nef / Beta-2-microglobulin / Protein Nef
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
Model detailsHLA-B0702 carrying RM9 peptide
AuthorsRizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H001085/1 United Kingdom
CitationJournal: Retrovirology / Year: 2015
Title: A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape.
Authors: Klverpris, H.N. / Cole, D.K. / Fuller, A. / Carlson, J. / Beck, K. / Schauenburg, A.J. / Rizkallah, P.J. / Buus, S. / Sewell, A.K. / Goulder, P.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 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

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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, B-7 alpha chain
B: Beta-2-microglobulin
C: Protein Nef
D: HLA class I histocompatibility antigen, B-7 alpha chain
E: Beta-2-microglobulin
F: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,53521
Polymers90,3306
Non-polymers1,20515
Water8,953497
1
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
C: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,72410
Polymers45,1653
Non-polymers5597
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-35 kcal/mol
Surface area19440 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, B-7 alpha chain
E: Beta-2-microglobulin
F: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,81211
Polymers45,1653
Non-polymers6478
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-18 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.270, 49.130, 107.460
Angle α, β, γ (deg.)91.370, 93.570, 95.750
Int Tables number1
Space group name H-MP1
DetailsChains A, B and C form one biological entity. A second copy in the a.u. is formed by chains D, E and F

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 32190.324 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: P01889
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Protein Nef / RM9


Mass: 1095.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q90VG9, UniProt: P03407*PLUS

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Non-polymers , 4 types, 512 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Sodium Cacodylate, pH 6, 15% PEG 8000, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.09→48.86 Å / Num. obs: 54249 / % possible obs: 97.5 % / Redundancy: 2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.087 / Net I/σ(I): 4.8 / Num. measured all: 107642
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.09-2.1420.3582801739350.8220.31795.7
9.35-48.862.10.0499.512866070.9930.0497.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.02 Å48.86 Å
Translation6.02 Å48.86 Å

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Processing

Software
NameVersionClassification
XDS0.1.16data reduction
Aimless2.5.5data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0049refinement
GDAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 2.09→48.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2393 / WRfactor Rwork: 0.185 / FOM work R set: 0.8298 / SU B: 10.564 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2055 / SU Rfree: 0.1789 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 2757 5.1 %RANDOM
Rwork0.1756 51450 --
obs0.1783 54207 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.82 Å2 / Biso mean: 51.539 Å2 / Biso min: 14.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.2 Å2-0.05 Å2
2---0.95 Å20.52 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 2.09→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6366 0 77 497 6940
Biso mean--41.16 47.35 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196665
X-RAY DIFFRACTIONr_bond_other_d0.0020.026006
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9449032
X-RAY DIFFRACTIONr_angle_other_deg0.92313832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36723.279369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.547151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3791568
X-RAY DIFFRACTIONr_chiral_restr0.110.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021642
X-RAY DIFFRACTIONr_mcbond_it1.2381.5143112
X-RAY DIFFRACTIONr_mcbond_other1.2381.5143111
X-RAY DIFFRACTIONr_mcangle_it2.0412.263890
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 194 -
Rwork0.226 3730 -
all-3924 -
obs--95.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.85460.857-0.32673.89210.60571.2458-0.0126-0.00780.0873-0.19460.0465-0.136-0.0617-0.024-0.03380.02040.0104-0.02590.038-0.0240.1628-10.243120.036525.7518
21.1133-0.4562-1.2971.08150.27727.57910.17141.0681-0.2273-1.0516-0.25190.1615-0.6191-0.59060.08051.187-0.1063-0.06631.2458-0.06590.3064-8.363826.8136-10.2436
34.95830.7726-3.30072.3221-1.78315.3483-0.2150.5293-0.3034-0.77850.0827-0.71860.21620.38740.13230.4154-0.08070.22970.3669-0.13420.4716.402617.11374.0128
42.0121-0.3182-0.34653.1865-0.11571.2033-0.0335-0.04880.10390.20490.02390.0755-0.15580.02360.00970.04840.0096-0.040.0368-0.0030.134716.262942.746544.6315
52.48270.7304-0.63782.8420.01166.59850.0305-1.0874-0.16761.3102-0.2447-0.2825-0.31750.88150.21421.012-0.0678-0.10680.7666-0.0060.324514.944748.799480.4696
63.28510.2716-2.89682.06640.87785.3934-0.1217-0.3727-0.14340.6591-0.01490.50580.1548-0.34110.13660.42880.0440.12580.33210.06550.33721.197136.490366.8167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 181
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 181
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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