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- PDB-7zt5: Structure of E8 TCR in complex in human MR1 bound to 3FSA -

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Basic information

Entry
Database: PDB / ID: 7zt5
TitleStructure of E8 TCR in complex in human MR1 bound to 3FSA
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / MR1 / TCR / 3-formylsalicylic 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 / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / 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 / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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
3-methanoyl-2-oxidanyl-benzoic acid / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKaruppiah, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)97,9565
Polymers97,7904
Non-polymers1661
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-40 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.970, 104.670, 117.700
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


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 , 2 types, 78 molecules

#5: Chemical ChemComp-7ZS / 3-methanoyl-2-oxidanyl-benzoic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris Propane pH 8.5, 20% PEG 3350

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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: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.09→58.85 Å / Num. obs: 67006 / % possible obs: 99.77 % / Redundancy: 15 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.024 / Rrim(I) all: 0.094 / Net I/σ(I): 14.9
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 13.6 % / Rmerge(I) obs: 4.97 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3210 / CC1/2: 0.344 / Rpim(I) all: 1.383 / Rrim(I) all: 5.164 / % possible all: 97.04

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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: 2.09→58.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 19.893 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26607 3384 5.1 %RANDOM
Rwork0.22507 ---
obs0.22714 63556 99.66 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--1.24 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.09→58.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 11 77 6510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136649
X-RAY DIFFRACTIONr_bond_other_d0.0030.0155961
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.6459036
X-RAY DIFFRACTIONr_angle_other_deg1.2031.5813745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28722.77379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.175151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4311538
X-RAY DIFFRACTIONr_chiral_restr0.060.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021627
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_it1.8163.9713180
X-RAY DIFFRACTIONr_mcbond_other1.8153.9713179
X-RAY DIFFRACTIONr_mcangle_it2.8635.9463966
X-RAY DIFFRACTIONr_mcangle_other2.8635.9463967
X-RAY DIFFRACTIONr_scbond_it1.8494.1573469
X-RAY DIFFRACTIONr_scbond_other1.8464.1563467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9166.1555068
X-RAY DIFFRACTIONr_long_range_B_refined4.82843.5796889
X-RAY DIFFRACTIONr_long_range_B_other4.82143.5676888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 242 -
Rwork0.427 4525 -
obs--97.33 %
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)
12.08220.2467-1.18891.2978-0.11241.89770.0380.0404-0.0962-0.2537-0.0069-0.3583-0.09670.0028-0.03110.41830.00910.09650.50280.00940.105919.23916.483-16.333
22.080.2182-0.10093.5470.45676.0342-0.19150.5054-0.2003-0.93180.01310.17570.329-0.25780.17830.5961-0.02530.04110.4809-0.01870.049513.85122.018-35.596
32.99990.2408-2.38431.4957-0.74376.1884-0.0126-0.2869-0.25770.3047-0.0459-0.01090.18890.08210.05850.2773-0.0522-0.06340.23260.05190.0442-2.5281.71530.446
41.66530.1921-0.62050.7078-0.69754.06620.0898-0.0334-0.0790.17280.00990.0906-0.1131-0.4205-0.09970.2654-0.01480.0020.28340.02680.0213-19.7886.81123.199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 269
2X-RAY DIFFRACTION2B0 - 98
3X-RAY DIFFRACTION3D4 - 189
4X-RAY DIFFRACTION4E1 - 242

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