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- PDB-4u1h: HLA class I micropolymorphisms determine peptide-HLA landscape an... -

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Basic information

Entry
Database: PDB / ID: 4u1h
TitleHLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Components
  • Beta-2-microglobulin
  • GAG protein
  • HLA class I histocompatibility antigen, B-7 alpha chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / HLA / HIV
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / 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 ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / 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 / viral process / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin / 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 / retroviral ribonuclease H / exoribonuclease H / cellular response to iron(III) ion / MHC class II protein complex / exoribonuclease H activity / 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 / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / protein processing / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / host multivesicular body / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / specific granule lumen / viral penetration into host nucleus / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-DNA hybrid ribonuclease activity / negative regulation of epithelial cell proliferation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / peptidase activity / host cell / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination
Similarity search - Function
gag protein p24 N-terminal domain / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin ...gag protein p24 N-terminal domain / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / Beta-2-microglobulin / GAG protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
Model detailsHLA-B0702 carrying TL9 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 / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / 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_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 2.2Oct 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, B-7 alpha chain
B: Beta-2-microglobulin
C: GAG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,06117
Polymers45,1023
Non-polymers95914
Water5,657314
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint22 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.000, 81.440, 110.060
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-7 alpha chain / MHC class I antigen B*7


Mass: 32190.324 Da / Num. of mol.: 1 / 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) / Variant (production host): Rosetta / References: UniProt: P01889
#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 / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide GAG protein / TL9 peptide


Mass: 1032.168 Da / Num. of mol.: 1 / Fragment: UNP residues 67-75 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q70A36, UniProt: P04585*PLUS

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Non-polymers , 3 types, 328 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22% PEG 4000 and 0.2 M ammonium sulphate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.59→55.03 Å / Num. obs: 62396 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Net I/σ(I): 16.5 / Num. measured all: 456801
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.59-1.6370.72533209945550.8110.293100
7.11-55.036.80.03744.555778190.9990.01599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.89 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å55.03 Å
Translation2.5 Å55.03 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0049refinement
GDAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4I4W

4i4w


Resolution: 1.59→55.03 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1932 / WRfactor Rwork: 0.1627 / FOM work R set: 0.8933 / SU B: 2.805 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0755 / SU Rfree: 0.0779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3157 5.1 %RANDOM
Rwork0.1638 59167 --
obs0.1654 62324 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.93 Å2 / Biso mean: 23.73 Å2 / Biso min: 8.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.59→55.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 62 314 3554
Biso mean--36.71 33.93 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193392
X-RAY DIFFRACTIONr_bond_other_d0.0010.023082
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9444590
X-RAY DIFFRACTIONr_angle_other_deg0.92237094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40423.316187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79815554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.971534
X-RAY DIFFRACTIONr_chiral_restr0.1270.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_mcbond_it1.271.1221574
X-RAY DIFFRACTIONr_mcbond_other1.2711.1221573
X-RAY DIFFRACTIONr_mcangle_it1.981.6761973
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 231 -
Rwork0.218 4319 -
all-4550 -
obs--99.98 %
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)
12.14020.0860.41021.5833-0.16240.90770.00030.18690.0533-0.10640.0081-0.0131-0.0122-0.0343-0.00840.00790.0020.00180.02250.00620.0023-4.690412.1631-31.0118
20.5756-0.2182-0.87981.41281.72226.21630.0103-0.01630.00960.0615-0.0410.049-0.1844-0.13170.03070.03660.0283-0.00530.06370.00670.0531-25.562115.4579-1.8929
33.72181.1156-1.73322.6628-0.93942.5103-0.15-0.3673-0.41390.144-0.04140.02690.2660.05940.19140.08320.01490.03630.06040.04610.0735-15.2102-2.9047-10.4836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99

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