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- PDB-7zt3: Structure of E8 TCR in complex in human MR1 K43A -

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Basic information

Entry
Database: PDB / ID: 7zt3
TitleStructure of E8 TCR in complex in human MR1 K43A
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / MR1 / TCR
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 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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / 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 / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / innate immune response / focal adhesion / 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 / 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
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: 2.4 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
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: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
D: TCR alpha
E: TCR beta


Theoretical massNumber of molelcules
Total (without water)97,7324
Polymers97,7324
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-42 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.240, 111.380, 143.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33724.766 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


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)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 15 % PEG 4000

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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: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→47.83 Å / Num. obs: 44778 / % possible obs: 99.97 % / Redundancy: 14.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.031 / Rrim(I) all: 0.122 / Net I/σ(I): 15.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.487 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2128 / CC1/2: 0.499 / Rpim(I) all: 0.463 / Rrim(I) all: 1.561 / % possible all: 96.55

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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: 2.4→44.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.804 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2211 4.9 %RANDOM
Rwork0.19074 ---
obs0.19303 42501 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0 Å2
2---0.29 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.4→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 0 231 6527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136504
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155840
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6458840
X-RAY DIFFRACTIONr_angle_other_deg1.2341.5813465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9675775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14122.818369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.957151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0751536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021582
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_it2.6354.4943115
X-RAY DIFFRACTIONr_mcbond_other2.6344.4943114
X-RAY DIFFRACTIONr_mcangle_it3.9566.7323879
X-RAY DIFFRACTIONr_mcangle_other3.9556.7323880
X-RAY DIFFRACTIONr_scbond_it3.2564.8033389
X-RAY DIFFRACTIONr_scbond_other3.2554.8033390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9857.0814960
X-RAY DIFFRACTIONr_long_range_B_refined6.81650.1286813
X-RAY DIFFRACTIONr_long_range_B_other6.81550.0316789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 149 -
Rwork0.307 3023 -
obs--97.6 %
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)
11.1764-0.699-0.37251.59520.86911.06270.0065-0.03460.03280.0147-0.0580.1977-0.1333-0.18940.05150.04880.02560.00060.0560.01220.066-7.8133-35.580920.6279
21.91870.45720.23564.92280.96614.093-0.0174-0.14980.21560.2046-0.1599-0.0007-0.27940.38540.17740.0672-0.0267-0.01950.10110.04410.0843-9.1314-16.728512.9175
33.4342-1.7564-1.12462.47790.7571.586-0.2614-0.2477-0.35220.19220.1854-0.22310.40930.26380.0760.13320.04030.00170.07320.02360.144423.7813-77.370120.1989
41.3763-1.2233-0.80322.12240.97480.7135-0.068-0.0392-0.09620.14810.1221-0.22330.0980.1143-0.05410.0220.0207-0.02820.0373-0.03570.104833.904-68.50145.6383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 270
2X-RAY DIFFRACTION2B0 - 98
3X-RAY DIFFRACTION3D1 - 187
4X-RAY DIFFRACTION4E2 - 241

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