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- PDB-7ndu: Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid -

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Basic information

Entry
Database: PDB / ID: 7ndu
TitleGag:02 TCR in complex with HLA-E featuring a non-natural amino acid
Components
  • Beta-2-microglobulin
  • Gag6V(276-284 H4C)
  • HLA class I histocompatibility antigen, alpha chain E
  • T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain
  • T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain
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 tolerance induction / natural killer cell lectin-like receptor binding ...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 tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / T cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / T cell receptor complex / 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 interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / MHC class I protein binding / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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
T cell receptor alpha joining 23 / T cell receptor alpha variable 4 / T cell receptor beta joining 1-2 / 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: 2.9 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 2.0Feb 16, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity_src_gen / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_formal_charge / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_common_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jul 27, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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(276-284 H4C)
DDD: T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain
EEE: T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)94,8775
Polymers94,8775
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-47 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.980, 88.980, 293.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 31911.172 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
#3: Protein/peptide Gag6V(276-284 H4C)


Mass: 1098.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Protein T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain / TR alpha chain TRAV27*01J42*01C*01


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,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
Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22.3% (w/v) PEG 1500, 89 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 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→61.597 Å / Num. obs: 27166 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.082 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 8.3 % / Rmerge(I) obs: 2.569 / Mean I/σ(I) obs: 1 / Num. unique obs: 1306 / CC1/2: 0.458 / Rpim(I) all: 0.933 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
DIALSdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NDQ

7ndq


Resolution: 2.9→61.597 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.22 / SU B: 58.028 / SU ML: 0.448 / Average fsc free: 0.7983 / Average fsc work: 0.8409 / Cross valid method: FREE R-VALUE / ESU R: 0.736 / ESU R Free: 0.448
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3015 1336 4.923 %
Rwork0.2419 25800 -
all0.245 --
obs-27136 99.823 %
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.718 Å2
Baniso -1Baniso -2Baniso -3
1-1.801 Å2-0 Å2-0 Å2
2--1.801 Å2-0 Å2
3----3.602 Å2
Refinement stepCycle: LAST / Resolution: 2.9→61.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 0 0 6529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136725
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176002
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.6539140
X-RAY DIFFRACTIONr_angle_other_deg1.1351.58213851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7525810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57422.211398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.164151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5291549
X-RAY DIFFRACTIONr_chiral_restr0.0580.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021643
X-RAY DIFFRACTIONr_nbd_refined0.2150.21199
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.25729
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23001
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2146
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0960.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.226
X-RAY DIFFRACTIONr_nbd_other0.1870.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.26
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.3781190.3881844X-RAY DIFFRACTION99.3421
2.975-3.0570.44950.3731820X-RAY DIFFRACTION100
3.057-3.1460.381880.3621768X-RAY DIFFRACTION99.9461
3.146-3.2420.321840.3111715X-RAY DIFFRACTION99.889
3.242-3.3490.389870.2871665X-RAY DIFFRACTION99.943
3.349-3.4660.383870.2611613X-RAY DIFFRACTION100
3.466-3.5970.314670.261602X-RAY DIFFRACTION99.9401
3.597-3.7440.307810.2521503X-RAY DIFFRACTION99.9369
3.744-3.910.325610.2291478X-RAY DIFFRACTION100
3.91-4.1010.285760.2051380X-RAY DIFFRACTION100
4.101-4.3230.292650.1881346X-RAY DIFFRACTION100
4.323-4.5850.228770.1831246X-RAY DIFFRACTION99.9245
4.585-4.9020.27520.1851203X-RAY DIFFRACTION99.7615
4.902-5.2940.273560.2131131X-RAY DIFFRACTION99.8318
5.294-5.7990.364480.241031X-RAY DIFFRACTION99.815
5.799-6.4830.272500.23945X-RAY DIFFRACTION99.8996
6.483-7.4860.308440.213853X-RAY DIFFRACTION99.556
7.486-9.1670.255520.212715X-RAY DIFFRACTION99.8698
9.167-12.9570.237260.243590X-RAY DIFFRACTION99.1948
12.957-61.5970.291210.285352X-RAY DIFFRACTION97.389
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)
10.85930.07540.15011.53781.0512.2-0.0095-0.04180.05490.0704-0.03040.0052-0.2297-0.21480.03990.1963-0.026-0.01150.333-0.00690.004432.230122.226648.037
22.49660.0706-1.61781.5741-1.00995.7348-0.01030.05810.0513-0.10870.0791-0.33850.04280.3795-0.06880.19310.0179-0.01550.2824-0.08770.139446.484915.10737.7121
30.4295-0.8282.18521.624-4.303511.4183-0.1047-0.02770.0030.09380.0816-0.0005-0.1778-0.21660.02310.4197-0.0467-0.00250.4236-0.0230.345332.300921.475667.78
41.13510.06910.09360.7702-0.19863.933-0.0187-0.3674-0.00760.2829-0.02720.2301-0.3618-0.76550.0460.57630.1048-0.00790.8313-0.07050.340921.593922.5826101.6134
50.94870.09120.2850.5252-0.7033.721-0.1478-0.19830.0220.30860.07210.1028-0.3703-0.34960.07570.42040.05140.00010.39110.00090.170540.957219.5323104.7014
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 - 204
5X-RAY DIFFRACTION5ALLEEE3 - 258

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