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- PDB-7r7v: Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived... -

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Basic information

Entry
Database: PDB / ID: 7r7v
TitleCrystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9
Components
  • Beta-2-microglobulin
  • GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP
  • MHC class I antigen
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MHC / T Cell Immunity / Antigen Presentation / HIV / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
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 / 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 / : ...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 / 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
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, X.L. / Tan, K.M. / Walker, B.D. / Wang, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 HL103526; R01 AI149704; 5UM1Al144462; P30 AI060354 United States
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide.
Authors: Li, X. / Singh, N.K. / Collins, D.R. / Ng, R. / Zhang, A. / Lamothe-Molina, P.A. / Shahinian, P. / Xu, S. / Tan, K. / Piechocka-Trocha, A. / Urbach, J.M. / Weber, J.K. / Gaiha, G.D. / Takou ...Authors: Li, X. / Singh, N.K. / Collins, D.R. / Ng, R. / Zhang, A. / Lamothe-Molina, P.A. / Shahinian, P. / Xu, S. / Tan, K. / Piechocka-Trocha, A. / Urbach, J.M. / Weber, J.K. / Gaiha, G.D. / Takou Mbah, O.C. / Huynh, T. / Cheever, S. / Chen, J. / Birnbaum, M. / Zhou, R. / Walker, B.D. / Wang, J.H.
History
DepositionJun 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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: GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4105
Polymers45,2263
Non-polymers1842
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-20 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.562, 81.964, 109.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen / MHC class I protein / HLA-B*5701 Heavy Chain


Mass: 32256.641 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S6BVK3
#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP


Mass: 1090.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 30% w/v PEG8000, 0.1 M sodium cacodylate trihydrate, pH 6.5
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 60774 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.053 / Rrim(I) all: 0.131 / Χ2: 1.604 / Net I/σ(I): 6.4 / Num. measured all: 336499
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.61.06130330.6310.4711.1640.68599.8
1.63-1.665.70.91630080.6860.4071.0050.71699.7
1.66-1.695.60.79130210.7230.3530.8680.73499.5
1.69-1.725.60.66230100.8080.2950.7260.77399.7
1.72-1.765.50.52330030.8610.2350.5750.83899.4
1.76-1.85.50.45130190.8830.2030.4960.87499.5
1.8-1.855.30.3729780.910.170.4090.9898.9
1.85-1.95.30.31529960.9280.1460.3481.10198.4
1.9-1.955.70.2630180.950.1150.2851.23799.6
1.95-2.025.70.22130340.9690.0980.2431.44599.6
2.02-2.095.70.19530150.9740.0860.2141.6199.6
2.09-2.175.60.17430370.9770.0770.1911.78299.6
2.17-2.275.60.15630330.9780.0690.1711.82499.5
2.27-2.395.20.14129620.9780.0650.1561.89297.1
2.39-2.545.80.13530790.9830.0590.1472.06599.7
2.54-2.745.80.12330580.9830.0540.1352.17999.8
2.74-3.015.60.11330820.9870.050.1242.45499.7
3.01-3.455.20.10530420.9860.0490.1162.8597.2
3.45-4.345.60.09631210.9890.0420.1053.03899.3
4.34-505.20.09432250.9870.0430.1032.95697.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A1M

1a1m


Resolution: 1.6→40.98 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 3003 4.95 %
Rwork0.1728 57713 -
obs0.1741 60716 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.5 Å2 / Biso mean: 30.4885 Å2 / Biso min: 11.91 Å2
Refinement stepCycle: final / Resolution: 1.6→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 12 401 3573
Biso mean--45.18 40.24 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.24991470.23082638278596
1.62-1.650.2281470.222127142861100
1.65-1.680.26751380.216127462884100
1.68-1.710.29311240.213327152839100
1.71-1.750.23371380.20727632901100
1.75-1.790.23441620.201526992861100
1.79-1.830.23661290.19652722285199
1.83-1.870.26521410.19912714285598
1.87-1.920.23331410.190127322873100
1.92-1.980.23461420.185627362878100
1.98-2.050.21531420.184427492891100
2.05-2.120.20061450.180127352880100
2.12-2.20.2171210.173927962917100
2.2-2.30.20471580.1722711286999
2.3-2.420.22431260.17582721284798
2.42-2.580.20971350.178727722907100
2.58-2.780.21831400.176827892929100
2.78-3.050.20831470.179327982945100
3.05-3.50.17981400.16382737287797
3.5-4.40.17211630.144928312994100
4.4-40.980.17031770.16472895307298

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