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- PDB-2mou: Solution structure of StAR-related lipid transfer domain protein ... -

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Basic information

Entry
Database: PDB / ID: 2mou
TitleSolution structure of StAR-related lipid transfer domain protein 6 (STARD6)
ComponentsStAR-related lipid transfer protein 6
KeywordsTRANSPORT PROTEIN / Steroidogenic acute regulatory protein (StAR) / START domain / Cholesterol metabolism / Steroidogenesis
Function / homology
Function and homology information


Pregnenolone biosynthesis / lipid transport / lipid binding
Similarity search - Function
StAR-related lipid transfer protein 5/6 / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
StAR-related lipid transfer protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsLetourneau, D. / Bedard, M. / Lefebvre, A. / Lehoux, J.G. / Lavigne, P.
CitationJournal: To be Published
Title: Solution structure of StAR-related lipid transfer domain protein 6 (STARD6)
Authors: Letourneau, D. / Bedard, M. / Lefebvre, A. / Lehoux, J.G. / Lavigne, P.
History
DepositionMay 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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_software.name
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: StAR-related lipid transfer protein 6


Theoretical massNumber of molelcules
Total (without water)25,0581
Polymers25,0581
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)20 / 1000Lowest energy, restraint violations and Ramachandran parameters
RepresentativeModel #1closest to the average

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Components

#1: Protein StAR-related lipid transfer protein 6 / START domain-containing protein 6 / StARD6


Mass: 25057.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NM_139171/NP_631910, STARD6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59095

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D C(CO)NH
1313D HNCO
1412D 1H-15N HSQC
1513D HN(CO)CA
1613D HNHA
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D (H)CCH-TOCSY
11012D 1H-13C HSQC
11113D 1H-13C NOESY aliphatic
11212D 1H-13C HSQC aromatic
11313D 1H-13C NOESY aromatic
11412D 1H-13C HSQC aliphatic

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] StAR_D6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: StAR_D6-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: 1.000 atm / Temperature: 298.150 K

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NMR measurement

NMR spectrometerType: Varian UnityInova / Manufacturer: Varian / Model: UnityInova / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Rieping, Habeck, Bardiaux, Bernard, Malliavi, Nilgesstructure calculation, refinement
CcpNmr Analysis2.2.2Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauedata analysis
DANGLE1.1Cheung, Maguire, Stevens, Broadhurstdihedral restraints from chemical shifts
NMRPipe2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxfile conversion
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation, refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: Lowest energy, restraint violations and Ramachandran parameters
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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