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- PDB-2hac: Structure of Zeta-Zeta Transmembrane Dimer -

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Basic information

Entry
Database: PDB / ID: 2hac
TitleStructure of Zeta-Zeta Transmembrane Dimer
ComponentsT-cell surface glycoprotein CD3 zeta chain
KeywordsMEMBRANE PROTEIN / transmembrane / alpha helix
Function / homology
Function and homology information


gamma-delta T cell receptor complex / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / Nef and signal transduction / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains ...gamma-delta T cell receptor complex / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / Nef and signal transduction / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / PD-1 signaling / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / protein complex oligomerization / T cell receptor signaling pathway / protein-containing complex assembly / adaptive immune response / cell surface receptor signaling pathway / protein heterodimerization activity / Golgi apparatus / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 zeta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChou, J.J. / Wucherpfennig, K.W. / Schnell, J.R. / Call, M.E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor.
Authors: Call, M.E. / Schnell, J.R. / Xu, C. / Lutz, R.A. / Chou, J.J. / Wucherpfennig, K.W.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD3 zeta chain
B: T-cell surface glycoprotein CD3 zeta chain


Theoretical massNumber of molelcules
Total (without water)7,5112
Polymers7,5112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide T-cell surface glycoprotein CD3 zeta chain / T-cell receptor T3 zeta chain


Mass: 3755.474 Da / Num. of mol.: 2 / Fragment: transmembrane region (28-60)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3Z, T3Z, TCRZ / Production host: Escherichia coli (E. coli) / References: UniProt: P20963

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111gradient-enhanced HNCA
1223D 15N-separated NOESY
1323D 15N-separated NOESY
1423D 13C-separated NOESY
1533D 15N-separated NOESY
164standard HSQC and TROSY-HSQC for D(NH) couplings; 2D (CA)CONH quantitative JCH experiment for D(CaHa) couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM disulfide crosslinked zeta-zeta dimer U-15N,U-13C,85%-2H. Sodium dodecyl sulfate (40 mM) and dodecyl phosphocholine (200 mM), 95% H2O, 5% D2O.95% H2O/5% D2O
20.5-1.0 mM disulfide crosslinked zeta-zeta dimer U-15N,U-13C. Sodium dodecyl sulfate (40 mM) and dodecyl phosphocholine (200 mM), 95% H2O, 5% D2O.95% H2O/5% D2O
30.5-1.0 mM disulfide crosslinked zeta-zeta dimer, mixed-label. One monomer: U-15N,U-2H. Other monomer: natural abundance isotopes. Sodium dodecyl sulfate (40 mM) and dodecyl phosphocholine (200 mM), 95% H2O, 5% D2O.95% H2O/5% D2O
40.5-1.0 mM disulfide crosslinked zeta-zeta dimer U-15N,U-13C. Sodium dodecyl sulfate (40 mM) and dodecyl phosphocholine (200 mM), 95% H2O, 5% D2O. 5% polyacrylamide gel.95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate buffer / pH: 7.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Frank Delaglioprocessing
CARA1.5Rochus Kellerdata analysis
XPLOR-NIH2.11Charles Schwietersrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 426 intramolecular NOE restraints, 46 intermolecular NOE restraints, 42 dihedral angle restraints, 70 residual dipolar coupling restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15

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