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- PDB-4nqe: Crystal structure of TCR-MR1 ternary complex bound to 5-(2-oxoeth... -

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Basic information

Entry
Database: PDB / ID: 4nqe
TitleCrystal structure of TCR-MR1 ternary complex bound to 5-(2-oxoethylideneamino)-6-D-ribitylaminouracil
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / immune complex / MR1 / TCR / Ig-domain / protein binding / Schiff base / membrane
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 / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / alpha-beta T cell activation / Generation of second messenger molecules ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / 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 / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Downstream TCR signaling / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / 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 / external side of plasma membrane / lysosomal membrane / innate immune response / 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
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 / 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 subtype / Immunoglobulin / 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
Chem-2L4 / T cell receptor beta constant 1 / Beta-2-microglobulin / TRA@ protein / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: Nature / Year: 2014
Title: T-cell activation by transitory neo-antigens derived from distinct microbial pathways.
Authors: Corbett, A.J. / Eckle, S.B. / Birkinshaw, R.W. / Liu, L. / Patel, O. / Mahony, J. / Chen, Z. / Reantragoon, R. / Meehan, B. / Cao, H. / Williamson, N.A. / Strugnell, R.A. / Van Sinderen, D. ...Authors: Corbett, A.J. / Eckle, S.B. / Birkinshaw, R.W. / Liu, L. / Patel, O. / Mahony, J. / Chen, Z. / Reantragoon, R. / Meehan, B. / Cao, H. / Williamson, N.A. / Strugnell, R.A. / Van Sinderen, D. / Mak, J.Y. / Fairlie, D.P. / Kjer-Nielsen, L. / Rossjohn, J. / McCluskey, J.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Structure summary
Revision 1.3Feb 19, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Major histocompatibility complex class I-related gene protein
D: TCR alpha
E: TCR beta
F: Beta-2-microglobulin
G: TCR alpha
H: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,94510
Polymers187,3138
Non-polymers6332
Water15,997888
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR alpha
H: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9735
Polymers93,6564
Non-polymers3161
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: TCR alpha
E: TCR beta
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9735
Polymers93,6564
Non-polymers3161
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.110, 70.600, 143.860
Angle α, β, γ (deg.)90.00, 104.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules ACBFDGEH

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


Mass: 31711.670 Da / Num. of mol.: 2
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 form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
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: 22650.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P4G7*PLUS
#4: Protein TCR beta


Mass: 27546.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS

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Non-polymers , 2 types, 890 molecules

#5: Chemical ChemComp-2L4 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxoethylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxoethylideneamino)-6-D-ribitylaminouracil


Mass: 316.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N4O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.3
Details: 12% (w/v) PEG3350, 0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.3, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→75.41 Å / Num. obs: 62837 / % possible obs: 98.6 % / Observed criterion σ(I): 8.1 / Biso Wilson estimate: 32.14 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9088 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 6147 5.03 %RANDOM
Rwork0.1821 ---
obs0.1841 -98.56 %-
Displacement parametersBiso mean: 38.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.8886 Å20 Å23.3591 Å2
2---9.4912 Å20 Å2
3---5.6027 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 2.1→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12375 0 42 888 13305
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112795HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0517425HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5691SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes305HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1867HARMONIC5
X-RAY DIFFRACTIONt_it12795HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1640SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14320SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2371 416 4.72 %
Rwork0.2152 8397 -
all0.2162 8813 -
obs--98.56 %

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