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- PDB-7r7y: Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived... -

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Basic information

Entry
Database: PDB / ID: 7r7y
TitleCrystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
Components
  • Beta-2-microglobulin
  • GLN-ALA-THR-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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / 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 / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal 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
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: 1.601 Å
AuthorsLi, X.L. / Ng, R. / 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 6, 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-THR-GLN-GLU-VAL-LYS-ASN-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8836
Polymers44,6073
Non-polymers2763
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-23 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.335, 81.828, 109.920
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 / Human Leukocyte Antigen B*57:01 / HLA-B*5701 Heavy Chain


Mass: 31736.172 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: U6BR87
#2: Protein Beta-2-microglobulin


Mass: 11766.198 Da / Num. of mol.: 1 / Fragment: UNP residues 22-119
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-THR-GLN-GLU-VAL-LYS-ASN-TRP


Mass: 1104.191 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 30% w/v PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, 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: Jun 4, 2014
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: 60505 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.028 / Rrim(I) all: 0.121 / Χ2: 4.894 / Net I/σ(I): 11.9 / Num. measured all: 1117738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6318.50.65729740.9560.1570.6761.724100
1.63-1.6618.60.57929810.9540.1380.5961.931100
1.66-1.6918.50.51729720.960.1230.5322.155100
1.69-1.7218.60.44729830.9690.1070.462.368100
1.72-1.7618.60.39529770.9720.0940.4072.509100
1.76-1.818.60.34230260.980.0810.3512.84100
1.8-1.8518.70.329870.9820.0710.3083.371100
1.85-1.918.60.26429630.9830.0630.2724.048100
1.9-1.9518.70.23130090.9870.0550.2384.944100
1.95-2.0218.70.19829990.9920.0470.2035.222100
2.02-2.0918.60.18430200.9920.0440.1896.009100
2.09-2.1718.70.16530070.9930.0390.1696.023100
2.17-2.2718.60.15229980.9940.0360.1566.245100
2.27-2.3918.60.1430490.9950.0330.1446.27100
2.39-2.5418.60.13330120.9950.0310.1366.542100
2.54-2.7418.50.12730400.9950.030.137.281100
2.74-3.0118.40.11430540.9960.0270.1178.097100
3.01-3.4518.10.0930840.9980.0220.0938.134100
3.45-4.3417.90.06531130.9990.0160.0666.985100
4.34-5017.50.0532570.9990.0120.0514.9599.5

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Processing

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

1a1m


Resolution: 1.601→33.804 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3031 5.02 %
Rwork0.153 57396 -
obs0.1549 60427 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 20.8334 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.601→33.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 18 570 3731
Biso mean--51.3 34.53 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093305
X-RAY DIFFRACTIONf_angle_d1.0754497
X-RAY DIFFRACTIONf_chiral_restr0.353457
X-RAY DIFFRACTIONf_plane_restr0.007592
X-RAY DIFFRACTIONf_dihedral_angle_d21.461256
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6012-1.62620.27321130.1947248596
1.6262-1.65280.2011310.17742572100
1.6528-1.68130.21181260.16422612100
1.6813-1.71190.20741260.15972585100
1.7119-1.74480.19611480.15522562100
1.7448-1.78040.17871680.15692565100
1.7804-1.81920.21221270.15572566100
1.8192-1.86150.17471370.15582613100
1.8615-1.9080.18061300.15912586100
1.908-1.95960.20371430.16012588100
1.9596-2.01730.22131300.15072592100
2.0173-2.08240.17381330.14232605100
2.0824-2.15680.20221290.15682600100
2.1568-2.24310.18761330.15032613100
2.2431-2.34520.18151350.15192613100
2.3452-2.46880.16611460.1552609100
2.4688-2.62340.18651470.15892609100
2.6234-2.82590.19851370.16192650100
2.8259-3.11010.18611420.16062629100
3.1101-3.55970.18611570.14672647100
3.5597-4.48320.16891520.12772678100
4.4832-33.80.19991410.15982817100

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