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- PDB-4nqd: Crystal structure of TCR-MR1 ternary complex and non-covalently b... -

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Basic information

Entry
Database: PDB / ID: 4nqd
TitleCrystal structure of TCR-MR1 ternary complex and non-covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / immune complex / MR1 / T-Cell receptor / 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 / antigen processing and presentation of peptide antigen via MHC class I / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling ...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 / antigen processing and presentation of peptide antigen via MHC class I / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / 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 / 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 / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / 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 / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / 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 / positive regulation of protein binding / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / 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 / Golgi apparatus / endoplasmic reticulum / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-Q87 / 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: 2.2 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 2.0Oct 30, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / struct_ref_seq_dif / struct_site
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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref_seq_dif.details / _struct_site.details / _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 chain
E: TCR beta chain
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,06611
Polymers187,3138
Non-polymers7533
Water9,818545
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7903
Polymers43,4602
Non-polymers3301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-10 kcal/mol
Surface area18220 Å2
MethodPISA
2
C: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7903
Polymers43,4602
Non-polymers3301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-9 kcal/mol
Surface area17390 Å2
MethodPISA
3
D: TCR alpha chain
E: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2893
Polymers50,1972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area20460 Å2
MethodPISA
4
G: TCR alpha chain
H: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)50,1972
Polymers50,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-27 kcal/mol
Surface area19540 Å2
MethodPISA
5
C: Major histocompatibility complex class I-related gene protein
D: TCR alpha chain
E: TCR beta chain
F: Beta-2-microglobulin
hetero molecules

A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,06611
Polymers187,3138
Non-polymers7533
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_447-x-1/2,y-1/2,-z+21
Buried area19430 Å2
ΔGint-101 kcal/mol
Surface area68500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.580, 68.874, 142.977
Angle α, β, γ (deg.)90.00, 104.21, 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, Beta-2 microglobulin, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein TCR alpha chain


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


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

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Non-polymers , 3 types, 548 molecules

#5: Chemical ChemComp-Q87 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol


Mass: 330.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O7
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 293 K / Method: 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, temperature 293K

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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: 2.2→50 Å / Num. obs: 101222 / % possible obs: 97.9 % / Observed criterion σ(I): 9.7 / Biso Wilson estimate: 38.25 Å2

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.51 Å / Cor.coef. Fo:Fc: 0.9339 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 5109 5.05 %RANDOM
Rwork0.1813 ---
obs0.1836 101214 97.69 %-
Displacement parametersBiso mean: 37.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.807 Å20 Å25.0475 Å2
2---8.667 Å20 Å2
3---6.8599 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12482 0 52 545 13079
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112928HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0817607HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5758SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes323HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1882HARMONIC5
X-RAY DIFFRACTIONt_it12928HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1648SEMIHARMONIC5
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_contact14491SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2436 353 4.79 %
Rwork0.2058 7023 -
all0.2076 7376 -
obs--97.69 %

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