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- PDB-8j8i: Membrane-bound structure of CD3z cytoplasmic domain -

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Basic information

Entry
Database: PDB / ID: 8j8i
TitleMembrane-bound structure of CD3z cytoplasmic domain
ComponentsT-cell surface glycoprotein CD3 zeta chain
KeywordsIMMUNE SYSTEM / T cell receptor / CD3z / ITAM / membrane-bound structure / phosphorylation pattern
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
AuthorsLi, H. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Membrane-bound structure of CD3z cytoplasmic domain
Authors: Li, H. / Xu, C.
History
DepositionMay 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)15,8861
Polymers15,8861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 15885.997 Da / Num. of mol.: 1 / Mutation: C8S, D12L,M72V,M95V,M104V,M134V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD247, 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-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic23D HNCO
141isotropic23D HNCA
151isotropic23D HN(CA)CB
161isotropic23D CBCA(CO)NH
171isotropic23D HBHA(CO)NH
181isotropic23D (H)CCH-TOCSY
191isotropic23D C(CO)NH
1101isotropic22D 1H-13C HSQC
1111isotropic22D 1H-15N HSQC
1121isotropic22D 1H-13C filtered-NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-100% 13C; U-100% 15N] CD3zTMCD, 20 mM None Bis-Tris, 60 mM None POPG, 90 % None H2O, 10 % None D2O, 90% H2O/10% D2O
Details: 0.3 mM 13C,15N-CD3zTMCD was reconstituted in 60 mM POPG, 20 mM Bis-Tris pH 6.7
Label: 13C15N_CD3zTMCD / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMCD3zTMCD[U-100% 13C; U-100% 15N]1
20 mMBis-TrisNone1
60 mMPOPGNone1
90 %H2ONone1
10 %D2ONone1
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
KUJIRARIKENchemical shift assignment
KUJIRARIKENpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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