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- PDB-8gvb: The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Ne... -

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Basic information

Entry
Database: PDB / ID: 8gvb
TitleThe complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 peptide
Components
  • 8-mer peptide from Protein Nef
  • Beta-2-microglobulin
  • MHC class I antigen
  • TD08 TCR alpha chain
  • TD08 TCR beta chain
KeywordsIMMUNE SYSTEM / Complex structure / Public TCRs / T cell immunity / Nef138-8 epitope
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 / 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, 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. ...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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGao, G.F. / Shi, Y. / Ma, K. / Chai, Y. / Guan, J. / Qi, J. / Tan, S. / Dong, T. / Iwamoto, A. / Kawana-Tachikawa, A.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFC2300700 China
CitationJournal: J Immunol. / Year: 2022
Title: Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors.
Authors: Ma, K. / Chai, Y. / Guan, J. / Tan, S. / Qi, J. / Kawana-Tachikawa, A. / Dong, T. / Iwamoto, A. / Shi, Y. / Gao, G.F.
History
DepositionSep 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TD08 TCR alpha chain
B: TD08 TCR beta chain
H: MHC class I antigen
L: Beta-2-microglobulin
P: 8-mer peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)96,0075
Polymers96,0075
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-53 kcal/mol
Surface area38500 Å2
Unit cell
Length a, b, c (Å)71.657, 71.657, 381.651
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein TD08 TCR alpha chain


Mass: 23132.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein TD08 TCR beta chain


Mass: 28271.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein MHC class I antigen


Mass: 31683.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: F6IQZ4
#4: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#5: Protein/peptide 8-mer peptide from Protein Nef


Mass: 1040.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.06 M divalent ions (MgCl2, CaCl2), 0.1 M Tris (pH 8.5), 0.1 M Bicine (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 19722 / % possible obs: 99.4 % / Redundancy: 14.8 % / Biso Wilson estimate: 70.02 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 19.031
Reflection shellResolution: 3.2→3.318 Å / Rmerge(I) obs: 2.172 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 19722 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.18.2_3874refinement
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXM

3vxm


Resolution: 3.2→35.01 Å / SU ML: 0.4472 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3208 759 4.64 %
Rwork0.2803 15601 -
obs0.2821 16360 82.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.58 Å2
Refinement stepCycle: LAST / Resolution: 3.2→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6462 0 0 0 6462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056628
X-RAY DIFFRACTIONf_angle_d0.63028981
X-RAY DIFFRACTIONf_chiral_restr0.0483932
X-RAY DIFFRACTIONf_plane_restr0.00351181
X-RAY DIFFRACTIONf_dihedral_angle_d13.67312435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.4191720.39011345X-RAY DIFFRACTION36.57
3.45-3.80.35431600.34312879X-RAY DIFFRACTION78.85
3.8-4.350.33831900.30433676X-RAY DIFFRACTION99.69
4.35-5.470.28061610.25093776X-RAY DIFFRACTION98.92
5.47-35.010.30441760.25153925X-RAY DIFFRACTION98.06
Refinement TLS params.Method: refined / Origin x: 13.0160272028 Å / Origin y: 6.86517231683 Å / Origin z: 31.0580074944 Å
111213212223313233
T0.173305403184 Å20.0923373173231 Å2-0.0581872503076 Å2-0.622204594496 Å20.0502975993751 Å2--0.406096285105 Å2
L1.26248617215 °2-0.207152324743 °2-0.382608438219 °2-1.2626946624 °20.935753113581 °2--3.20482818732 °2
S0.268971082431 Å °-0.367641936852 Å °-0.282842898031 Å °0.254829334311 Å °0.0189974488448 Å °-0.125541834897 Å °0.623082581357 Å °0.0159344521873 Å °-0.142310606218 Å °
Refinement TLS groupSelection details: all

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