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- PDB-2rsg: Solution structure of the CERT PH domain -

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Basic information

Entry
Database: PDB / ID: 2rsg
TitleSolution structure of the CERT PH domain
ComponentsCollagen type IV alpha-3-binding protein
KeywordsLIPID TRANSPORT / pleckstrin homology
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / : / ceramide binding / Sphingolipid de novo biosynthesis / intermembrane lipid transfer ...intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / : / ceramide binding / Sphingolipid de novo biosynthesis / intermembrane lipid transfer / ceramide metabolic process / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / response to endoplasmic reticulum stress / muscle contraction / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
STARD11, START domain / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...STARD11, START domain / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailsclosest to the average, model 1
AuthorsSugiki, T. / Takeuchi, K. / Tokunaga, Y. / Kumagai, K. / Kawano, M. / Nishijima, M. / Hanada, K. / Takahashi, H. / Shimada, I.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for the Golgi association by the pleckstrin homology domain of the ceramide trafficking protein (CERT)
Authors: Sugiki, T. / Takeuchi, K. / Yamaji, T. / Takano, T. / Tokunaga, Y. / Kumagai, K. / Hanada, K. / Takahashi, H. / Shimada, I.
History
DepositionFeb 25, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen type IV alpha-3-binding protein


Theoretical massNumber of molelcules
Total (without water)11,1801
Polymers11,1801
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Collagen type IV alpha-3-binding protein / Ceramide transfer protein / hCERT / Goodpasture antigen-binding protein / GPBP / START domain- ...Ceramide transfer protein / hCERT / Goodpasture antigen-binding protein / GPBP / START domain-containing protein 11 / StARD11 / StAR-related lipid transfer protein 11


Mass: 11180.384 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A3BP, CERT, STARD11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5P4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D HNCO
1523D HN(CO)CA
1613D 1H-15N NOESY
1724D 13C 15N NOESY
1823D (H)CCH-TOCSY
1922D 1H-13C HSQC
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-98% 15N] CERT-1, 10 mM HEPES-2, 100 mM sodium chloride-3, 5 mM DTT-4, 93% H2O/7% D2O93% H2O/7% D2O
20.2 mM [U-98% 13C; U-98% 15N] CERT-5, 10 mM HEPES-6, 100 mM sodium chloride-7, 5 mM DTT-8, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMCERT-1[U-98% 15N]1
10 mMHEPES-21
100 mMsodium chloride-31
5 mMDTT-41
0.2 mMCERT-5[U-98% 13C; U-98% 15N]2
10 mMHEPES-62
100 mMsodium chloride-72
5 mMDTT-82
Sample conditionspH: 7.20 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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