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- PDB-7ndq: Gag:02 TCR in complex with HLA-E. -

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Basic information

Entry
Database: PDB / ID: 7ndq
TitleGag:02 TCR in complex with HLA-E.
Components
  • Beta-2-microglobulin
  • Gag6V
  • HLA class I histocompatibility antigen, alpha chain E
  • T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain
  • TCR Gag:02-alpha,TCR Gag:02-alpha,TCR Gag:02-alpha
KeywordsIMMUNE SYSTEM / TCR-pHLA complex / non-natural amino acid
Function / homology
Function and homology information


MHC protein binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction ...MHC protein binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / T cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of immunoglobulin production / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / immune system process / T cell receptor binding / negative regulation of T cell proliferation / 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 / lumenal side of endoplasmic reticulum membrane / response to bacterium / 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 / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / cell surface receptor signaling pathway
Similarity search - Function
: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Gag protein p6 / Gag protein p6 / 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 ...: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Gag protein p6 / Gag protein p6 / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Immunoglobulin V-set domain / : / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
T cell receptor alpha joining 23 / T cell receptor alpha variable 4 / T cell receptor beta joining 1-2 / Truncated gag protein / Human nkt tcr beta chain / T cell receptor beta variable 7-9 / M1-specific T cell receptor alpha chain / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsPengelly, R.J. / Robinson, R.A.
CitationJournal: Eur.J.Immunol. / Year: 2022
Title: Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition.
Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / ...Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / Grant, T. / Dembek, M. / Verma, A. / Gibbs-Howe, D. / Blicher, T.H. / Knox, A. / Robinson, R.A. / Cole, D.K. / Leonard, S.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jul 27, 2022Group: Derived calculations / Category: atom_type / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 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
AAA: HLA class I histocompatibility antigen, alpha chain E
BBB: Beta-2-microglobulin
CCC: Gag6V
DDD: TCR Gag:02-alpha,TCR Gag:02-alpha,TCR Gag:02-alpha
EEE: T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)94,8895
Polymers94,8895
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-51 kcal/mol
Surface area38970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.391, 89.391, 293.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 4 types, 4 molecules AAABBBDDDEEE

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31955.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: 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
#4: Protein TCR Gag:02-alpha,TCR Gag:02-alpha,TCR Gag:02-alpha / T cell receptor alpha variable 4 / T cell receptor alpha joining 23 / TR alpha chain ...T cell receptor alpha variable 4 / T cell receptor alpha joining 23 / TR alpha chain TRAV27*01J42*01C*01 / M1-specific T cell receptor alpha chain


Mass: 22074.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV4, TRAJ23, TRA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0B4J268, UniProt: A0A075B6U7, UniProt: P0DSE1
#5: Protein T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain / T cell receptor beta variable 7-9 / T cell receptor beta joining 1-2 / Human nkt tcr beta chain


Mass: 27913.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV7-9, TRBJ1-2, B2M, HDCMA22P / Production host: Escherichia coli (E. coli)
References: UniProt: P04435, UniProt: A0A0J9YX06, UniProt: K7N5M4

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Protein/peptide / Non-polymers , 2 types, 14 molecules CCC

#3: Protein/peptide Gag6V / Gag polyprotein / Matrix protein p17 / Nucleocapsid protein p7 / Pr55Gag / p6-gag / Capsid protein p24


Mass: 1066.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: B6S6I4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 23.2% (w/v) PEG 1500, 93 mM MMT pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→85.354 Å / Num. obs: 39941 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.041 / Net I/σ(I): 11.6
Reflection shellResolution: 2.55→2.59 Å / Rmerge(I) obs: 6.926 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1932 / CC1/2: 0.735 / Rpim(I) all: 1.343

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W1W, 5EU6

5w1w

5eu6


Resolution: 2.551→76.445 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.197 / SU B: 50.437 / SU ML: 0.424 / Average fsc free: 0.7878 / Average fsc work: 0.8046 / Cross valid method: FREE R-VALUE / ESU R: 0.468 / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2963 1945 4.882 %
Rwork0.2397 37892 -
all0.242 --
obs-39837 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 90.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0 Å2
2--0.47 Å2-0 Å2
3----0.941 Å2
Refinement stepCycle: LAST / Resolution: 2.551→76.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 0 13 6557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136742
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176027
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6519162
X-RAY DIFFRACTIONr_angle_other_deg1.1361.58213908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8355811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26122.2400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.008151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.781549
X-RAY DIFFRACTIONr_chiral_restr0.0570.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027753
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021657
X-RAY DIFFRACTIONr_nbd_refined0.2080.21244
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.25734
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.217
X-RAY DIFFRACTIONr_nbd_other0.2530.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.24
X-RAY DIFFRACTIONr_mcbond_it1.9324.8573247
X-RAY DIFFRACTIONr_mcbond_other1.9314.8563246
X-RAY DIFFRACTIONr_mcangle_it3.237.2794051
X-RAY DIFFRACTIONr_mcangle_other3.237.2794052
X-RAY DIFFRACTIONr_scbond_it1.6714.9863495
X-RAY DIFFRACTIONr_scbond_other1.6714.9853493
X-RAY DIFFRACTIONr_scangle_it2.8627.4165109
X-RAY DIFFRACTIONr_scangle_other2.8627.4165109
X-RAY DIFFRACTIONr_lrange_it5.05853.7937109
X-RAY DIFFRACTIONr_lrange_other5.05753.7877109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.551-2.6170.4591350.4212719X-RAY DIFFRACTION99.6856
2.617-2.6890.4641330.4142699X-RAY DIFFRACTION99.9647
2.689-2.7670.4491310.3992586X-RAY DIFFRACTION100
2.767-2.8520.3871290.382533X-RAY DIFFRACTION100
2.852-2.9450.3371100.3482486X-RAY DIFFRACTION100
2.945-3.0490.3841420.3262350X-RAY DIFFRACTION99.9599
3.049-3.1640.3371130.3232332X-RAY DIFFRACTION100
3.164-3.2930.3281080.2822222X-RAY DIFFRACTION100
3.293-3.440.3011100.2492146X-RAY DIFFRACTION100
3.44-3.6070.276990.2372041X-RAY DIFFRACTION100
3.607-3.8020.301890.2311964X-RAY DIFFRACTION100
3.802-4.0330.3061090.2141854X-RAY DIFFRACTION100
4.033-4.3110.263930.2061745X-RAY DIFFRACTION100
4.311-4.6570.266970.1791632X-RAY DIFFRACTION100
4.657-5.1010.222870.1631505X-RAY DIFFRACTION100
5.101-5.7030.264750.1941386X-RAY DIFFRACTION100
5.703-6.5850.288610.221243X-RAY DIFFRACTION100
6.585-8.0640.275550.2081072X-RAY DIFFRACTION100
8.064-11.40.236440.173854X-RAY DIFFRACTION100
11.4-76.4450.366250.333523X-RAY DIFFRACTION99.8178
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)
11.3055-0.04520.29271.29350.47843.416-0.0591-0.12140.1658-0.0872-0.060.0856-0.3874-0.11770.11910.5325-0.04540.01390.4059-0.02080.030531.255822.297347.4502
23.2005-0.0162-2.30882.7823-1.45495.1829-0.02980.1018-0.129-0.0078-0.0009-0.5063-0.10770.26110.03060.5951-0.05490.0280.4867-0.07980.139745.506114.892237.4736
32.1826-3.8954-1.40387.03031.86037.557-0.1434-0.16020.0460.27140.1987-0.0732-0.1489-0.056-0.05530.3993-0.0138-0.10780.6836-0.0580.129331.254421.176767.4141
40.5278-0.50930.30520.8908-1.18984.9122-0.051-0.354-0.23510.25010.09870.4423-0.1916-0.4949-0.04780.6979-0.03310.02731.0688-0.07720.420321.454823.6712101.9615
51.3821-0.3069-0.08430.9836-0.53173.2678-0.1175-0.32560.11120.2973-0.01230.0563-0.1882-0.0580.12970.5545-0.0076-0.01710.6716-0.00950.035340.952120.7468104.2947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 276
2X-RAY DIFFRACTION2ALLBBB0 - 99
3X-RAY DIFFRACTION3ALLCCC1 - 9
4X-RAY DIFFRACTION4ALLDDD3 - 205
5X-RAY DIFFRACTION5ALLEEE3 - 258

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