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- PDB-5a4h: Solution structure of the lipid droplet anchoring peptide of CGI-... -

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Basic information

Entry
Database: PDB / ID: 5a4h
TitleSolution structure of the lipid droplet anchoring peptide of CGI-58 bound to DPC micelles
Components1-ACYLGLYCEROL-3-PHOSPHATE O-ACYLTRANSFERASE ABHD5
KeywordsTRANSFERASE / CGI-58 / ABHD5 / LIPID DROPLET ANCHOR / SOLUTION STRUCTURE
Function / homology
Function and homology information


1-acylglycerol-3-phosphate O-acyltransferase / lysophosphatidic acid acyltransferase activity / 1-acylglycerol-3-phosphate O-acyltransferase activity / positive regulation of triglyceride catabolic process / phosphatidic acid biosynthetic process / positive regulation of lipid catabolic process / positive regulation of lipoprotein lipase activity / carboxylic ester hydrolase activity / negative regulation of sequestering of triglyceride / lipid homeostasis ...1-acylglycerol-3-phosphate O-acyltransferase / lysophosphatidic acid acyltransferase activity / 1-acylglycerol-3-phosphate O-acyltransferase activity / positive regulation of triglyceride catabolic process / phosphatidic acid biosynthetic process / positive regulation of lipid catabolic process / positive regulation of lipoprotein lipase activity / carboxylic ester hydrolase activity / negative regulation of sequestering of triglyceride / lipid homeostasis / lipid droplet / fatty acid metabolic process / lipid metabolic process / cell differentiation / cytosol
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
1-acylglycerol-3-phosphate O-acyltransferase ABHD5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsBoeszoermenyi, A. / Arthanari, H. / Wagner, G. / Nagy, H.M. / Zangger, K. / Lindermuth, H. / Oberer, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of a Cgi-58 Motif Provides the Molecular Basis of Lipid Droplet Anchoring.
Authors: Boeszoermenyi, A. / Nagy, H.M. / Arthanari, H. / Pillip, C.J. / Lindermuth, H. / Luna, R.E. / Wagner, G. / Zechner, R. / Zangger, K. / Oberer, M.
History
DepositionJun 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references / Other
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-ACYLGLYCEROL-3-PHOSPHATE O-ACYLTRANSFERASE ABHD5


Theoretical massNumber of molelcules
Total (without water)3,9811
Polymers3,9811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide 1-ACYLGLYCEROL-3-PHOSPHATE O-ACYLTRANSFERASE ABHD5 / ABHYDROLASE DOMAIN-CONTAINING PROTEIN 5 / LIPID DROPLET-BINDING PROTEIN CGI-58 / PROTEIN CGI-58 / WR10_43


Mass: 3981.318 Da / Num. of mol.: 1 / Fragment: N-TERMINAL PEPTIDE, RESIDUES 10-43
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL LD BINDING MOTIF OF CGI-58 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PSUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9DBL9, 1-acylglycerol-3-phosphate O-acyltransferase
Sequence detailsN-TERMINAL FRAMGENT (V10-K43). FIRST FIVE RESIDUES ARE ARTIFACTS FROM CLONING AND PROTEASE CLEAVAGE ...N-TERMINAL FRAMGENT (V10-K43). FIRST FIVE RESIDUES ARE ARTIFACTS FROM CLONING AND PROTEASE CLEAVAGE SITE. THEY ARE NOT PART OF NATIVE STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CA)CB
131HN(CA)CO
141HSQC
251HSQC ANOESY
261NOESYHSQC
371H(CCO)NH
481C(CO)NH
491(H)CCH TOCSY
5101TOCSY 90MS
611113CHSQC B900
6121CNOESY B900
7131NOESY 200MS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON THE DOUBLY LABELED PEPTIDE BOUND TO DPC MICELLES. HOMONOCULEAR NOESY AND TOCSY EXPERIMENTS ON A SHORTER UNLABELED PEPTIDE ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON THE DOUBLY LABELED PEPTIDE BOUND TO DPC MICELLES. HOMONOCULEAR NOESY AND TOCSY EXPERIMENTS ON A SHORTER UNLABELED PEPTIDE ALSO BOUND TO DPC MICELLES AND PARAMAGNETIC RELAXATION EXPERIMENTS TO ORIENT THE PEPTIDE WITH RESPECT TO THE MICELLE.

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Sample preparation

Details
Solution-IDContents
193% H2O/7% D2O
2100% D2O
393% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
170.0 6.0 1.0 atm310.0 K
270.0 6.0 1.0 atm310.0 K
370.0 6.0 1.0 atm310.0 K
470.0 6.0 1.0 atm310.0 K
570.0 6.0 1.0 atm303.0 K
670.0 6.0 1.0 atm310.0 K
770.0 6.0 1.0 atm303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DD2BrukerDD26001
Varian7002
Bruker7503
Varian5004
Bruker9005
Bruker9006
Bruker9007

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGUNTERTrefinement
NMRDrawANYstructure solution
NMRPipeANYstructure solution
CcpNmr Analysis2.4structure solution
TALOS1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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