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- PDB-7zt8: Structure of E8 TCR in complex in human MR1 bound to 3FBA -

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Basic information

Entry
Database: PDB / ID: 7zt8
TitleStructure of E8 TCR in complex in human MR1 bound to 3FBA
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / MR1 / TCR / 3-formylbenzoic acid
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / 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 / membrane / identical protein binding / 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. / Immunoglobulin C-Type / Immunoglobulin C1-set ...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
3-methylbenzoic acid / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKaruppiah, V. / Srikannathasan, V. / Robinson, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Exp.Med. / Year: 2023
Title: Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses.
Authors: Chancellor, A. / Alan Simmons, R. / Khanolkar, R.C. / Nosi, V. / Beshirova, A. / Berloffa, G. / Colombo, R. / Karuppiah, V. / Pentier, J.M. / Tubb, V. / Ghadbane, H. / Suckling, R.J. / Page, ...Authors: Chancellor, A. / Alan Simmons, R. / Khanolkar, R.C. / Nosi, V. / Beshirova, A. / Berloffa, G. / Colombo, R. / Karuppiah, V. / Pentier, J.M. / Tubb, V. / Ghadbane, H. / Suckling, R.J. / Page, K. / Crean, R.M. / Vacchini, A. / De Gregorio, C. / Schaefer, V. / Constantin, D. / Gligoris, T. / Lloyd, A. / Hock, M. / Srikannathasan, V. / Robinson, R.A. / Besra, G.S. / van der Kamp, M.W. / Mori, L. / Calogero, R. / Cole, D.K. / De Libero, G. / Lepore, M.
History
DepositionMay 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 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
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
D: TCR alpha
E: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1977
Polymers97,7904
Non-polymers4073
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-34 kcal/mol
Surface area36610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.600, 113.130, 143.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 33782.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin / 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 TCR alpha


Mass: 22884.367 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)
#4: Protein TCR beta


Mass: 29243.314 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)

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Non-polymers , 4 types, 147 molecules

#5: Chemical ChemComp-OVV / 3-methylbenzoic acid / M-Toluic acid


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium acetate tetrahydrate, 0.1 M MOPS pH 7.5, 12 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 51936 / % possible obs: 100 % / Redundancy: 15.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.062 / Rrim(I) all: 0.241 / Net I/σ(I): 9.5
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 14.9 % / Rmerge(I) obs: 3.158 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2591 / CC1/2: 0.494 / Rpim(I) all: 0.842 / Rrim(I) all: 0.327 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U6Q

5u6q


Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.998 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26285 2550 4.9 %RANDOM
Rwork0.21079 ---
obs0.21335 49318 99.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.187 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å2-0 Å2
2---2.51 Å20 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 27 144 6515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136578
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155892
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.6458932
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5813592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2985783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75622.788373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.808151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.191537
X-RAY DIFFRACTIONr_chiral_restr0.0680.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027502
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021604
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2664.0113141
X-RAY DIFFRACTIONr_mcbond_other4.2664.0113140
X-RAY DIFFRACTIONr_mcangle_it5.926.0073918
X-RAY DIFFRACTIONr_mcangle_other5.9196.0083919
X-RAY DIFFRACTIONr_scbond_it4.9724.3383437
X-RAY DIFFRACTIONr_scbond_other4.9724.3393438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8036.365014
X-RAY DIFFRACTIONr_long_range_B_refined8.40144.9896946
X-RAY DIFFRACTIONr_long_range_B_other8.40144.9676938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 193 -
Rwork0.362 3583 -
obs--99.97 %
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)
11.2529-1.03650.54291.7142-0.83181.10580.0064-0.00650.0438-0.062-0.0598-0.25050.08550.17310.05340.16260.00310.01490.0373-0.00250.14317.4109-20.458720.7311
21.76120.4847-0.7283.1607-0.86764.8215-0.1422-0.0954-0.24110.14340.02330.0780.2769-0.70260.11890.1756-0.02650.01560.1797-0.05290.1228.99-39.897813.3571
32.0504-1.58040.60222.6916-0.69151.409-0.1195-0.18320.13290.1620.12320.1341-0.1439-0.2373-0.00370.1292-0.00030.00850.0544-0.02390.0738-23.340621.91219.664
41.0434-0.85330.47071.6679-0.35380.4539-0.0211-0.02130.02360.0690.04890.1915-0.0092-0.0921-0.02780.0998-0.00950.01120.03340.01540.0844-33.238913.15895.2814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 301
2X-RAY DIFFRACTION2B0 - 98
3X-RAY DIFFRACTION3D1 - 201
4X-RAY DIFFRACTION4E2 - 242

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