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- PDB-4u1s: HLA class I micropolymorphisms determine peptide-HLA landscape an... -

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Basic information

Entry
Database: PDB / ID: 4u1s
TitleHLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-81 alpha chain
  • Vpr protein
KeywordsIMMUNE SYSTEM / Immunoglobulin / HLA / HIV
Function / homology
Function and homology information


Vpr-mediated induction of apoptosis by mitochondrial outer membrane permeabilization / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host cell cycle progression / biological process involved in interaction with host / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / negative regulation of DNA repair / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA ...Vpr-mediated induction of apoptosis by mitochondrial outer membrane permeabilization / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host cell cycle progression / biological process involved in interaction with host / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / negative regulation of DNA repair / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / 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 / viral life cycle / secretory granule membrane / 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 / symbiont-mediated activation of host apoptosis / 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 / defense response / 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 / protein homooligomerization / 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 / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / virion component / viral penetration into host nucleus / specific granule lumen / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / host cell / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / monoatomic ion transmembrane transport / protein homotetramerization / molecular adaptor activity / adaptive immune response / host extracellular space / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein / 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 / : ...Retroviral VpR/VpX protein / VPR/VPX protein / 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, B alpha chain / Beta-2-microglobulin / Protein Vpr / HLA class I histocompatibility antigen, B alpha chain / Vpr protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
Model detailsHLA-B4201 carrying FL9 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 16, 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
Revision 2.2Nov 13, 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, B-81 alpha chain
B: Beta-2-microglobulin
C: Vpr protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,08217
Polymers45,1493
Non-polymers93314
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-2 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.170, 81.250, 110.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsChains A, B and C form one biological entity. Only one copy is present in the a.u.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-81 alpha chain / B'DT / MHC class I antigen B*81


Mass: 32145.348 Da / Num. of mol.: 1 / Fragment: UNP residues 25-301
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: Q31610, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / 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, 1 molecules C

#3: Protein/peptide Vpr protein / FL9


Mass: 1124.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: T2D0U8, UniProt: P69726*PLUS

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Non-polymers , 4 types, 258 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M Lithium Chloride, pH 8, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.76→40.625 Å / Num. all: 46617 / Num. obs: 46617 / % possible obs: 100 % / Redundancy: 7.9 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.109 / Rsym value: 0.096 / Net I/av σ(I): 5.773 / Net I/σ(I): 16.1 / Num. measured all: 370026
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.76-1.8181.0140.62721733990.3961.0143.1100
1.81-1.868.10.7770.72658332930.3010.7774100
1.86-1.918.10.60212616532400.2340.6025100
1.91-1.978.10.431.42520931270.1670.437100
1.97-2.038.10.351.72448330360.1360.358.5100
2.03-2.18.10.2782.12366429320.1090.27810.4100
2.1-2.1880.2292.62305228690.090.22911.9100
2.18-2.278.10.1963.12182027080.0760.19613.7100
2.27-2.3780.1593.82120726500.0620.15915.7100
2.37-2.4980.144.42022825340.0550.1417.1100
2.49-2.627.90.1195.21889524020.0480.11918.6100
2.62-2.787.80.0986.41782222800.040.09821100
2.78-2.977.70.0788.21657821430.0320.07823.899.9
2.97-3.217.80.066101573220250.0260.06626.999.9
3.21-3.527.80.05511.81433318440.0220.05531.2100
3.52-3.947.60.04812.81287617030.020.04833.8100
3.94-4.5480.04413.61196715010.0170.04437.3100
4.54-5.577.80.04313.71013412940.0170.04337100
5.57-7.877.70.04612.6783710240.0190.04634.8100
7.87-40.6256.90.04411.842246130.0190.04435.899

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.63 Å
Translation2.5 Å40.63 Å

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Processing

Software
NameVersionClassification
XDS3.3.20data reduction
SCALA2.1.4data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0049refinement
GDAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 1.76→40.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2032 / WRfactor Rwork: 0.1716 / FOM work R set: 0.8755 / SU B: 4.547 / SU ML: 0.073 / SU R Cruickshank DPI: 0.107 / SU Rfree: 0.1044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 2350 5 %RANDOM
Rwork0.175 44192 --
obs0.1766 46542 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 27.041 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20 Å2
2---0.13 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.76→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 59 244 3488
Biso mean--39 32.66 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193354
X-RAY DIFFRACTIONr_bond_other_d0.0010.023036
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9444536
X-RAY DIFFRACTIONr_angle_other_deg0.9536984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39623.204181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1421532
X-RAY DIFFRACTIONr_chiral_restr0.1380.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
X-RAY DIFFRACTIONr_mcbond_it1.411.2631560
X-RAY DIFFRACTIONr_mcbond_other1.4111.2631559
X-RAY DIFFRACTIONr_mcangle_it2.2181.8821950
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 158 -
Rwork0.226 3224 -
all-3382 -
obs--99.79 %
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)
12.5271-0.116-0.63291.92870.33821.22790.02470.2509-0.0892-0.16920.00660.0560.0088-0.0191-0.03130.01670.0029-0.00750.0289-0.00760.0134.8133-12.0665-31.1346
20.3006-0.39131.25961.1716-0.90786.62460.05540.0481-0.04120.12820.0135-0.02120.46950.3716-0.06890.09550.0389-0.01870.1639-0.03360.097125.6612-15.2537-1.7498
33.85281.14061.80692.41210.76732.8228-0.0699-0.37050.52730.1384-0.04270.0682-0.32780.02740.11260.0832-0.00940.01140.086-0.08860.116115.05212.9405-10.5723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 181
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 277
4X-RAY DIFFRACTION3B0 - 99

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