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- PDB-2l35: Structure of the DAP12-NKG2C transmembrane heterotrimer -

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Basic information

Entry
Database: PDB / ID: 2l35
TitleStructure of the DAP12-NKG2C transmembrane heterotrimer
Components
  • DAP12-NKG2C_TM
  • TYRO protein tyrosine kinase-binding protein
KeywordsPROTEIN BINDING / Immunoreceptor / transmembrane assembly / DAP12-NKG2C complex
Function / homology
Function and homology information


myeloid leukocyte activation / positive regulation of receptor localization to synapse / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / negative regulation of transforming growth factor beta1 production / positive regulation of natural killer cell activation / positive regulation of microglial cell mediated cytotoxicity / Other semaphorin interactions ...myeloid leukocyte activation / positive regulation of receptor localization to synapse / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / negative regulation of transforming growth factor beta1 production / positive regulation of natural killer cell activation / positive regulation of microglial cell mediated cytotoxicity / Other semaphorin interactions / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 / amyloid-beta clearance / semaphorin-plexin signaling pathway / negative regulation of long-term synaptic potentiation / response to axon injury / cellular defense response / forebrain development / osteoclast differentiation / secretory granule membrane / positive regulation of superoxide anion generation / DAP12 interactions / positive regulation of interleukin-1 beta production / positive regulation of interleukin-6 production / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / DAP12 signaling / actin cytoskeleton organization / protein-macromolecule adaptor activity / molecular adaptor activity / protein stabilization / intracellular signal transduction / signaling receptor binding / positive regulation of gene expression / Neutrophil degranulation / 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 / YojJ-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
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
Revision 1.2Nov 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 / 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

Downloads & links

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Assembly

Deposited unit
A: DAP12-NKG2C_TM
B: TYRO protein tyrosine kinase-binding protein


Theoretical massNumber of molelcules
Total (without water)9,6972
Polymers9,6972
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 DAP12-NKG2C_TM


Mass: 6478.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF DAP12 (RESIDUES 1-33) AND NKG2C (RESIDUES 35-63)
Source: (gene. exp.) Homo sapiens (human) / Gene: TYROBP, DAP12, KARAP / Production host: Escherichia coli (E. coli) / References: UniProt: O43914
#2: Protein/peptide TYRO protein tyrosine kinase-binding protein / DNAX-activation protein 12 / Killer-activating receptor-associated protein / KAR-associated protein


Mass: 3217.884 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 35-66
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
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
1232D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HN(COCA)CB
1733D 1H-15N NOESY
1833D 1H-13C NOESY
1953D 1H-15N NOESY
11052D 1H-13C HSQC
11122D 1H-15N HSQC
11242D 1H-13C HSQC
11323D HNCA
11423D HN(CO)CA
11523D HN(CA)CB
11623D HN(COCA)CB
11743D 1H-15N NOESY
11843D 1H-13C NOESY
11963D 1H-15N NOESY
12062D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N; U-80% 2H] DAP12-NKG2C TM-1, 0.5-1 mM DAP12 TM-2, 25 mM SDS-3, 250 mM Foscholine-14-4, 20 mM sodium phosphate-5, 95% H2O/5% D2O95% H2O/5% D2O
20.5-1 mM DAP12-NKG2C TM-6, 0.5-1 mM [U-100% 13C; U-100% 15N; U-80% 2H] DAP12 TM-7, 25 mM SDS-8, 250 mM Foscholine-14-9, 20 mM sodium phosphate-10, 95% H2O/5% D2O95% H2O/5% D2O
30.5-1 mM [U-100% 13C; U-100% 15N] DAP12-NKG2C TM-11, 0.5-1 mM DAP12 TM-12, 25 mM [U-100% 2H] SDS-13, 250 mM [U-100% 2H] Foscholine-14-14, 20 mM sodium phosphate-15, 95% H2O/5% D2O95% H2O/5% D2O
40.5-1 mM DAP12-NKG2C TM-16, 0.5-1 mM [U-100% 13C; U-100% 15N] DAP12 TM-17, 25 mM [U-100% 2H] SDS-18, 250 mM [U-100% 2H] Foscholine-14-19, 20 mM sodium phosphate-20, 95% H2O/5% D2O95% H2O/5% D2O
50.5-1 mM [U-100% 15N; U-100% 2H] DAP12-NKG2C TM-21, 0.5-1 mM [U-10% 13C] DAP12 TM-22, 25 mM [U-100% 2H] SDS-23, 250 mM [U-100% 2H] Foscholine-14-24, 20 mM sodium phosphate-25, 95% H2O/5% D2O95% H2O/5% D2O
60.5-1 mM [U-10% 13C] DAP12-NKG2C TM-26, 0.5-1 mM [U-100% 15N; U-90% 2H] DAP12 TM-27, 25 mM [U-100% 2H] SDS-28, 250 mM [U-100% 2H] Foscholine-14-29, 20 mM sodium phosphate-30, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDAP12-NKG2C TM-1[U-100% 13C; U-100% 15N; U-80% 2H]0.5-11
mMDAP12 TM-20.5-11
25 mMSDS-31
250 mMFoscholine-14-41
20 mMsodium phosphate-51
mMDAP12-NKG2C TM-60.5-12
mMDAP12 TM-7[U-100% 13C; U-100% 15N; U-80% 2H]0.5-12
25 mMSDS-82
250 mMFoscholine-14-92
20 mMsodium phosphate-102
mMDAP12-NKG2C TM-11[U-100% 13C; U-100% 15N]0.5-13
mMDAP12 TM-120.5-13
25 mMSDS-13[U-100% 2H]3
250 mMFoscholine-14-14[U-100% 2H]3
20 mMsodium phosphate-153
mMDAP12-NKG2C TM-160.5-14
mMDAP12 TM-17[U-100% 13C; U-100% 15N]0.5-14
25 mMSDS-18[U-100% 2H]4
250 mMFoscholine-14-19[U-100% 2H]4
20 mMsodium phosphate-204
mMDAP12-NKG2C TM-21[U-100% 15N; U-100% 2H]0.5-15
mMDAP12 TM-22[U-10% 13C]0.5-15
25 mMSDS-23[U-100% 2H]5
250 mMFoscholine-14-24[U-100% 2H]5
20 mMsodium phosphate-255
mMDAP12-NKG2C TM-26[U-10% 13C]0.5-16
mMDAP12 TM-27[U-100% 15N; U-90% 2H]0.5-16
25 mMSDS-28[U-100% 2H]6
250 mMFoscholine-14-29[U-100% 2H]6
20 mMsodium phosphate-306
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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