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- PDB-6vqz: HLA-B*27:05 presenting an HIV-1 6mer peptide -

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Basic information

Entry
Database: PDB / ID: 6vqz
TitleHLA-B*27:05 presenting an HIV-1 6mer peptide
Components
  • 6-mer peptide
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen / Human Immunodeficiency Virus
Function / homology
Function and homology information


integrase activity / 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 ...integrase activity / 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 / antigen processing and presentation of peptide antigen via MHC class I / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / 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 / 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 / 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 / host multivesicular body / 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 / 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 / viral penetration into host nucleus / RNA stem-loop binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / MHC class II protein complex binding / 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 / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / Golgi membrane
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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, alpha chain, C-terminal / MHC_I C-terminus / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
ARGININE / MHC class I antigen / Gag-Pol polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. ...Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Hansjorg, S. / Van Endert, P. / Harkiolaki, M. / Iversen, A.K.N.
CitationJournal: Cell Rep / Year: 2022
Title: Epitope length variants balance protective immune responses and viral escape in HIV-1 infection
Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, ...Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Schild, H. / van Endert, P. / Harkiolaki, M. / Iversen, A.K.
History
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
G: 6-mer peptide
F: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3638
Polymers89,0136
Non-polymers3502
Water2,072115
1
A: MHC class I antigen
B: Beta-2-microglobulin
F: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6824
Polymers44,5063
Non-polymers1751
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-13 kcal/mol
Surface area19180 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
G: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6824
Polymers44,5063
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-10 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.495, 130.516, 90.170
Angle α, β, γ (deg.)90.000, 104.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain F
23chain G
14chain C
24chain A

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUchain AAA1 - 2751 - 275
21GLYGLYGLUGLUchain CCC1 - 2751 - 275
12ILEILEMETMETchain BBB1 - 991 - 99
22ILEILEMETMETchain DDD1 - 991 - 99
13LYSLYSLEULEUchain FFF1 - 61 - 6
23LYSLYSLEULEUchain GGE1 - 61 - 6
14GLYGLYGLYGLYchain XCC11
24HISHISHISHISchain YAA33

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein MHC class I antigen


Mass: 31928.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: O78189
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 6-mer peptide


Mass: 830.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.44
ReflectionResolution: 2.25→130.49 Å / Num. obs: 47317 / % possible obs: 98.1 % / Redundancy: 2.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
2.25-2.372.60.4092.368300.84397.1
7.12-130.492.50.02913.715580.99898.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W0V

1w0v


Resolution: 2.25→87.333 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.88 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2437 2305 4.88 %
Rwork0.2006 44999 -
obs0.2037 47275 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.77 Å2 / Biso mean: 38.2333 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 2.25→87.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 49 115 6426
Biso mean--35 31.25 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046594
X-RAY DIFFRACTIONf_angle_d0.7868955
X-RAY DIFFRACTIONf_chiral_restr0.034914
X-RAY DIFFRACTIONf_plane_restr0.0041185
X-RAY DIFFRACTIONf_dihedral_angle_d13.1392477
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2493X-RAY DIFFRACTION7.446TORSIONAL
12C2493X-RAY DIFFRACTION7.446TORSIONAL
21B918X-RAY DIFFRACTION7.446TORSIONAL
22D918X-RAY DIFFRACTION7.446TORSIONAL
31F84X-RAY DIFFRACTION7.446TORSIONAL
32G84X-RAY DIFFRACTION7.446TORSIONAL
41C4X-RAY DIFFRACTION7.446TORSIONAL
42A4X-RAY DIFFRACTION7.446TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.29890.35271520.29682731288391
2.2989-2.35240.32141560.29852764292093
2.3524-2.41120.31511320.29672776290891
2.4112-2.47640.30191430.28052795293893
2.4764-2.54930.2831390.2772775291492
2.5493-2.63150.31691600.27482809296993
2.6315-2.72550.32571150.26462819293494
2.7255-2.83460.27991420.25092835297793
2.8346-2.96350.32331460.24912760290694
2.9635-3.11970.24581280.21692857298594
3.1197-3.3150.23361380.21122812295094
3.315-3.57070.28181440.20122829297393
3.5707-3.92960.22751500.17022824297494
3.9296-4.49720.21610.14342841300294
4.4972-5.6620.15141310.13722874300595
5.662-34.62670.18131230.15392898302194

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