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- PDB-7vu5: Structure of the transmembrane domain of the CD28 dimer -

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Basic information

Entry
Database: PDB / ID: 7vu5
TitleStructure of the transmembrane domain of the CD28 dimer
ComponentsT-cell-specific surface glycoprotein CD28
KeywordsIMMUNE SYSTEM / CD28 / transmembrane domain
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / positive regulation of isotype switching to IgG isotypes / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / Co-stimulation by CD28 ...Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / positive regulation of isotype switching to IgG isotypes / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of interleukin-4 production / humoral immune response / positive regulation of interleukin-10 production / immunological synapse / CD28 dependent PI3K/Akt signaling / positive regulation of viral genome replication / coreceptor activity / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / T cell activation / positive regulation of translation / positive regulation of cytokine production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of gene expression / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, H. / Cao, R. / Wen, M. / Ouyang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2022
Title: Structural characterization of a dimerization interface in the CD28 transmembrane domain.
Authors: Wu, H. / Cao, R. / Wen, M. / Xue, H. / OuYang, B.
History
DepositionNov 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell-specific surface glycoprotein CD28
B: T-cell-specific surface glycoprotein CD28


Theoretical massNumber of molelcules
Total (without water)9,3312
Polymers9,3312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area910 Å2
ΔGint-11 kcal/mol
Surface area8170 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 10015
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide T-cell-specific surface glycoprotein CD28 / TP44


Mass: 4665.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD28 / Production host: Escherichia coli (E. coli) / References: UniProt: P10747

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1TROSY-HSQC
121isotropic1TROSY-HNCO
131isotropic1TROSY-HN(CA)CO
141isotropic1TROSY-HNCA
151isotropic1TROSY-HN(CO)CA
161isotropic1TROSY-HN(CA)CB
172isotropic23D 1H-15N NOESY
1102isotropic23D 1H-13C NOESY
193isotropic23D 1H-15N NOESY
184isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.6 mM U-13C; U-15N; 75%-2H CD28_TM, 25 mM MES, 30 mM DMPC, 60 mM DHPC, 90% H2O/10% D2OU-13C; U-15N; 75%-2H_sampleU-13C; U-15N; 75%-2H_sample90% H2O/10% D2O
bicelle20.6 mM [U-13C; U-15N] CD28_TM, 25 mM MES, 30 mM acyl chain U-2H DMPC, 60 mM acyl chain U-2H DHPC, 90% H2O/10% D2OU-13C; U-15N_sampleU-13C; U-15N_sample90% H2O/10% D2O
bicelle30.6 mM U-15N; U-2H CD28_TM, 0.6 mM [U-13C] CD28_TM, 25 mM MES, 30 mM acyl chain U-2H DMPC, 60 mM acyl chain U-2H DHPC, 90% H2O/10% D2OU-15N,U-2H and U-13C_mixU-15N,U-2H and U-13C_mix90% H2O/10% D2O
bicelle40.2 mM U-15N; 15%-13C CD28_TM, 25 mM MES, 30 mM acyl chain U-2H DMPC, 60 mM acyl chain U-2H DHPC, 90% H2O/10% D2O0.2 mM [U-15N; U-2H; 15%-13C] Transmembrane Domain of CD28U-15N; 15%-13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCD28_TMU-13C; U-15N; 75%-2H1
25 mMMESnatural abundance1
30 mMDMPCnatural abundance1
60 mMDHPCnatural abundance1
0.6 mMCD28_TM[U-13C; U-15N]2
25 mMMESnatural abundance2
30 mMDMPCacyl chain U-2H2
60 mMDHPCacyl chain U-2H2
0.6 mMCD28_TMU-15N; U-2H3
25 mMMESnatural abundance3
30 mMDMPCacyl chain U-2H3
60 mMDHPCacyl chain U-2H3
0.2 mMCD28_TMU-15N; 15%-13C4
25 mMMESnatural abundance4
30 mMDMPCacyl chain U-2H4
60 mMDHPCacyl chain U-2H4
Sample conditionsIonic strength: 25 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.44Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.44Schwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 15 / Conformers calculated total number: 100 / Conformers submitted total number: 15

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