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- PDB-7r7x: Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived... -

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Basic information

Entry
Database: PDB / ID: 7r7x
TitleCrystal structure of HLA-B*5701 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


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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / 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 / 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 / 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 / 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 / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / : ...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
ISOPROPYL ALCOHOL / 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: 2.099 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 1.3Nov 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
E: GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP
F: GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2198
Polymers89,9646
Non-polymers2552
Water10,323573
1
A: MHC class I antigen
B: Beta-2-microglobulin
E: GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2375
Polymers44,9823
Non-polymers2552
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-16 kcal/mol
Surface area19020 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
F: GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)44,9823
Polymers44,9823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-16 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.540, 82.577, 157.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 32012.461 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U6BR87
#2: Protein 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP


Mass: 1090.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)

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Non-polymers , 3 types, 575 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 15-20% w/v PEG4000, 20% w/v 2-propanol, 0.1 M MES, pH 6.5

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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: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 53731 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.08 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Χ2: 0.819 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1860.67652850.8210.2940.740.66399.3
2.18-2.266.30.54752600.8720.2350.5970.66999.8
2.26-2.376.40.45453150.9030.1940.4950.671100
2.37-2.496.40.34953300.940.1490.3810.696100
2.49-2.656.40.26553310.9650.1130.2890.7100
2.65-2.856.40.18753420.9820.080.2040.771100
2.85-3.146.40.12653520.990.0530.1370.966100
3.14-3.596.30.07754130.9960.0330.0841.151100
3.59-4.526.10.04654380.9980.020.051.00399.9
4.52-506.10.03556650.9990.0150.0390.88699.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A1M

1a1m


Resolution: 2.099→39.936 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 2677 4.99 %
Rwork0.1835 50980 -
obs0.1852 53657 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 34.2725 Å2 / Biso min: 10.64 Å2
Refinement stepCycle: final / Resolution: 2.099→39.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 16 573 6909
Biso mean--71.12 40.59 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046523
X-RAY DIFFRACTIONf_angle_d0.6588863
X-RAY DIFFRACTIONf_chiral_restr0.046900
X-RAY DIFFRACTIONf_plane_restr0.0031166
X-RAY DIFFRACTIONf_dihedral_angle_d23.592437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0992-2.13730.26691400.2342260099
2.1373-2.17840.28941470.2285266099
2.1784-2.22290.25891270.22642647100
2.2229-2.27120.31021430.21932638100
2.2712-2.32410.26171480.21672652100
2.3241-2.38220.29061300.21762664100
2.3822-2.44660.28911450.21312655100
2.4466-2.51860.27391410.20372650100
2.5186-2.59980.21171340.19942660100
2.5998-2.69270.22421450.2022680100
2.6927-2.80050.27261300.2032668100
2.8005-2.92790.19391480.20322681100
2.9279-3.08230.24571330.20522676100
3.0823-3.27530.24061390.19182693100
3.2753-3.5280.22061510.18982680100
3.528-3.88280.21111360.1652727100
3.8828-4.4440.17261460.14272722100
4.444-5.59660.16221440.1398274199
5.5966-39.930.18031500.17222886100

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