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- PDB-2l34: Structure of the DAP12 transmembrane homodimer -

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Basic information

Entry
Database: PDB / ID: 2l34
TitleStructure of the DAP12 transmembrane homodimer
ComponentsTYRO protein tyrosine kinase-binding protein
KeywordsPROTEIN BINDING / Immunoreceptor / transmembrane assembly / DAP12
Function / homology
Function and homology information


myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / Other semaphorin interactions / positive regulation of microglial cell mediated cytotoxicity ...myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / Other semaphorin interactions / positive regulation of microglial cell mediated cytotoxicity / neutrophil activation involved in immune response / positive regulation of protein localization to cell surface / apoptotic cell clearance / Signal regulatory protein family interactions / negative regulation of type I interferon production / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / stimulatory C-type lectin receptor signaling pathway / negative regulation of long-term synaptic potentiation / response to axon injury / cellular defense response / forebrain development / osteoclast differentiation / positive regulation of superoxide anion generation / secretory granule membrane / positive regulation of interleukin-1 beta production / DAP12 interactions / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / actin cytoskeleton organization / molecular adaptor activity / protein stabilization / intracellular signal transduction / signaling receptor binding / Neutrophil degranulation / positive regulation of gene expression / cell surface / signal transduction / protein homodimerization activity / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
TYRO protein tyrosine kinase-binding protein
Similarity search - Domain/homology
TYRO protein tyrosine kinase-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsCall, M.E. / Wucherpfennig, K.W. / Chou, J.J.
CitationJournal: Nat.Immunol. / Year: 2010
Title: The structural basis for intramembrane assembly of an activating immunoreceptor complex.
Authors: Call, M.E. / Wucherpfennig, K.W. / Chou, J.J.
History
DepositionSep 6, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYRO protein tyrosine kinase-binding protein
B: TYRO protein tyrosine kinase-binding protein


Theoretical massNumber of molelcules
Total (without water)6,6622
Polymers6,6622
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)15 / 75structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide TYRO protein tyrosine kinase-binding protein / DNAX-activation protein 12 / Killer-activating receptor-associated protein / KAR-associated protein


Mass: 3331.042 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYROBP, DAP12, KARAP / Production host: Escherichia coli (E. coli) / References: UniProt: O43914

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HN(COCA)CB
1723D 1H-15N NOESY
1823D 1H-13C NOESY
1933D 1H-15N NOESY
11042D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 (dimer) mM [U-100% 13C; U-100% 15N; U-80% 2H] DAP12 transmembrane peptide-1, 20 mM sodium phosphate-2, 25 mM SDS-3, 250 mM Foscholine-14-4, 95% H2O/5% D2O95% H2O/5% D2O
20.5 (dimer) mM [U-100% 13C; U-100% 15N] DAP12 transmembrane peptide-5, 20 mM sodium phosphate-6, 25 mM [U-100% 2H] SDS-7, 250 mM [U-100% 2H] Foscholine-14-8, 95% H2O/5% D2O95% H2O/5% D2O
30.5 (monomer) mM [U-100% 15N; U-100% 2H] DAP12 transmembrane peptide-9, 0.5 (monomer) mM [U-100% 13C] DAP12 transmembrane peptide-10, 25 mM [U-100% 2H] SDS-11, 250 mM [U-100% 2H] Foscholine-14-12, 20 mM sodium phosphate-13, 95% H2O/5% D2O95% H2O/5% D2O
40.5 (dimer) mM [U-10% 13C] DAP12 transmembrane peptide-14, 25 mM [U-100% 2H] SDS-15, 250 mM [U-100% 2H] Foscholine-14-16, 20 mM sodium phosphate-17, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDAP12 transmembrane peptide-1[U-100% 13C; U-100% 15N; U-80% 2H]1
20 mMsodium phosphate-21
25 mMSDS-31
250 mMFoscholine-14-41
0.5 mMDAP12 transmembrane peptide-5[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-62
25 mMSDS-7[U-100% 2H]2
250 mMFoscholine-14-8[U-100% 2H]2
0.5 mMDAP12 transmembrane peptide-9[U-100% 15N; U-100% 2H]3
0.5 mMDAP12 transmembrane peptide-10[U-100% 13C]3
25 mMSDS-11[U-100% 2H]3
250 mMFoscholine-14-12[U-100% 2H]3
20 mMsodium phosphate-133
0.5 mMDAP12 transmembrane peptide-14[U-10% 13C]4
25 mMSDS-15[U-100% 2H]4
250 mMFoscholine-14-16[U-100% 2H]4
20 mMsodium phosphate-174
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 15 / Representative conformer: 1

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