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

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Basic information

Entry
Database: PDB / ID: 8gvg
TitleThe complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 (2F) peptide
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • TD08 TCR alpha chain
  • TD08 TCR beta chain
  • mutated 8-mer peptide from Protein Nef
KeywordsIMMUNE SYSTEM / Complex structure / Public TCRs / T cell immunity / Nef138-8 (2F) epitope
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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 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 15, 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_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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: mutated 8-mer peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)95,9915
Polymers95,9915
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-59 kcal/mol
Surface area39010 Å2
Unit cell
Length a, b, c (Å)71.035, 71.035, 383.869
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 mutated 8-mer peptide from Protein Nef


Mass: 1024.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV whole-genome vector AA1305#18 (others)
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: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium sulfate, 0.1 M Bis-Tris Propane (pH 7.5), 20% PEG 3350

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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: Jan 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.36→50 Å / Num. obs: 16829 / % possible obs: 98.9 % / Redundancy: 16.9 % / Biso Wilson estimate: 94.4 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 22.933
Reflection shellResolution: 3.36→3.48 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 5.539 / Num. unique obs: 16829 / Rsym value: 0.968 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.18.2_3874refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXM

3vxm


Resolution: 3.37→40.94 Å / SU ML: 0.918 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 48.5006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3199 818 5.19 %
Rwork0.2993 14949 -
obs0.3004 15767 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 148.21 Å2
Refinement stepCycle: LAST / Resolution: 3.37→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 0 0 6655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236831
X-RAY DIFFRACTIONf_angle_d0.50469262
X-RAY DIFFRACTIONf_chiral_restr0.0397960
X-RAY DIFFRACTIONf_plane_restr0.00391220
X-RAY DIFFRACTIONf_dihedral_angle_d15.79862504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.37-3.580.65921430.62752179X-RAY DIFFRACTION84.87
3.58-3.850.54121340.53452237X-RAY DIFFRACTION85.78
3.85-4.240.37981340.39962319X-RAY DIFFRACTION88.49
4.24-4.850.28391280.25762639X-RAY DIFFRACTION99.6
4.85-6.110.26221260.2632724X-RAY DIFFRACTION99.96
6.11-40.940.23491530.21912851X-RAY DIFFRACTION99.17
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.86888159130.304430140768-0.3463779646643.00326594823-0.191883013943.705604637290.2165868435950.2832325063740.490290772734-0.754311419733-0.1842981190790.246828331176-0.6649686598810.2557265127520.04618076565080.8619911679590.180546181964-0.004210603086230.8220749827090.1870382189610.926810681791-9.686387317633.870886391870.468286345414
21.5789494988-0.7480040098160.0767418202061.76842603253-0.2456163451352.754160402160.375691622547-0.1290954068020.9924334211960.543789197581-0.1883111363010.171304182502-1.967081130990.244269985912-0.0349000623571.921281983350.07251037181720.2068359817460.9231835691550.05681341001461.41509414381-12.266998681916.979864970114.6832818433
30.9094975031942.042720672430.4685661077494.607351650361.049577089480.234252323032-0.171230878989-0.522496767778-1.645342376291.22810198355-0.313945179659-0.519478088209-1.648304908840.8100084236930.4250345096660.8804710756380.552521881790.1527112129981.949632602140.3958935371210.920260536949-19.3451504074-13.044829282636.855489641
40.860435745537-0.7747369807111.720410149522.25096105995-1.711594734233.017403237990.250797756498-0.323922075816-0.3879302805620.04843102624350.1578032141130.3125458906810.2076173855910.0476010238319-0.3757536909490.87458385532-0.008513943556370.009260974850651.229634894540.1333460357671.07731091451-14.9628175052-26.220885469849.886174979
53.35298451479-0.03628170329970.6851849511761.19458457421-0.1125154379822.21416568866-0.067015210263-0.607842351658-0.1449730854630.8646808662040.2015485956560.102480329175-0.427989000868-0.523733218429-0.1119135774031.234688005130.158770494805-0.04299132723761.558550508230.1926325220451.09671141828-12.2053209228-21.43330517368.0095564717
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA3 - 2051 - 203
22chain BBB4 - 2451 - 240
33chain PPE1 - 81 - 8
44chain HHC1 - 2741 - 274
55chain LLD1 - 991 - 99

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