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- PDB-2mim: NMR structure of the chicken CD3 epsilon delta/gamma heterodimer -

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Basic information

Entry
Database: PDB / ID: 2mim
TitleNMR structure of the chicken CD3 epsilon delta/gamma heterodimer
ComponentsCD3 epsilon protein,CD3 glycoprotein
KeywordsIMMUNE SYSTEM / immune signalling subunit / CD3 / TCR
Function / homology
Function and homology information


alpha-beta T cell receptor complex / positive thymic T cell selection / T cell receptor binding / transmembrane signaling receptor activity / cell surface receptor signaling pathway / external side of plasma membrane
Similarity search - Function
CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain / CD3 glycoprotein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHeadey, S. / Berry, R. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of the chicken CD3 epsilon delta / gamma heterodimer and its assembly with the alpha beta T cell receptor
Authors: Berry, R. / Headey, S.J. / Call, M.J. / McCluskey, J. / Tregaskes, C.A. / Kaufman, J. / Koh, R. / Scanlon, M.J. / Call, M.E. / Rossjohn, J.
History
DepositionDec 15, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Structure summary
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Jan 23, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD3 epsilon protein,CD3 glycoprotein


Theoretical massNumber of molelcules
Total (without water)19,5701
Polymers19,5701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein CD3 epsilon protein,CD3 glycoprotein / CD3e protein / CD3D antigen delta / CD3g/d protein


Mass: 19569.771 Da / Num. of mol.: 1
Fragment: chicken CD3 epsilon domain (UNP residues 24-91),chicken CD3 gamma-delta domain (UNP residues 18-97)
Source method: isolated from a genetically manipulated source
Details: chimera of CD3 epsilon protein, LINKER, CD3 glycoprotein
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CD3 epsilon, cd3e, cd3g, CD3D, d / Production host: Escherichia coli (E. coli) / References: UniProt: P70069, UniProt: Q90768
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(COCA)CB
1323D HN(CA)CB
1413D H(CCO)NH
1513D HNCA
1613D HNCO
1723D HN(CO)CA
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-98% 13C; U-98% 15N] protein-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] protein-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-98% 13C; U-98% 15N]1
0.5 mMprotein-2[U-100% 13C; U-100% 15N; U-80% 2H]2
Sample conditionsIonic strength: 0.3 / pH: 7.6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
XEASYBartels et al.data analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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