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- PDB-2d8c: Solution structure of the sam-domain of mouse phosphatidyl cerami... -

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Basic information

Entry
Database: PDB / ID: 2d8c
TitleSolution structure of the sam-domain of mouse phosphatidyl ceramidecholinephosphotransferase 1
ComponentsPhosphatidylcholine:ceramide cholinephosphotransferase 1
KeywordsTRANSFERASE / CELL-FREE PROTEIN SYNTHESIS / PROTEIN REGULATION / LIPID METABOLISM / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


sphingomyelin synthase / Sphingolipid de novo biosynthesis / ceramide phosphoethanolamine synthase activity / sphingomyelin synthase activity / ceramide cholinephosphotransferase activity / : / : / Golgi trans cisterna / sphingomyelin biosynthetic process / sphingolipid biosynthetic process ...sphingomyelin synthase / Sphingolipid de novo biosynthesis / ceramide phosphoethanolamine synthase activity / sphingomyelin synthase activity / ceramide cholinephosphotransferase activity / : / : / Golgi trans cisterna / sphingomyelin biosynthetic process / sphingolipid biosynthetic process / ceramide biosynthetic process / plasma membrane => GO:0005886 / negative regulation of extrinsic apoptotic signaling pathway / cellular response to tumor necrosis factor / kinase activity / cellular response to lipopolysaccharide / inflammatory response / apoptotic process / positive regulation of gene expression / endoplasmic reticulum / nucleus / plasma membrane
Similarity search - Function
Sphingomyelin synthase-like domain / PAP2 superfamily C-terminal / Transcription Factor, Ets-1 / SAM domain profile. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylcholine:ceramide cholinephosphotransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Kigawa, T. / Koshiba, S. / Tomizawa, T. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the sam-domain of mouse phosphatidyl ceramidecholinephosphotransferase 1
Authors: Goroncy, A.K. / Kigawa, T. / Koshiba, S. / Tomizawa, T. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S.
History
DepositionDec 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: 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: Phosphatidylcholine:ceramide cholinephosphotransferase 1


Theoretical massNumber of molelcules
Total (without water)10,9541
Polymers10,9541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Phosphatidylcholine:ceramide cholinephosphotransferase 1 / Transmembrane protein 23 / Sphingomyelin synthase 1 / Mob protein


Mass: 10954.358 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: 9530058O11Rik / Plasmid: P041101-13
References: UniProt: Q8VCQ6, Transferases; Transferring phosphorus-containing groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.51mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17PETER GUNTERT ET AL.refinement
CYANA2.0.17PETER GUNTERT ET AL.structure solution
XwinNMR3.5BRUKERcollection
NMRPipe20020425FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.899aNAOHIRO KOBAYASHIdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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