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- PDB-2kyt: Solution structure of the H-REV107 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2kyt
TitleSolution structure of the H-REV107 N-terminal domain
ComponentsGroup XVI phospholipase A2
KeywordsHYDROLASE / H-REV107 / tumor suppressor / phospholipase / N-terminal domain
Function / homology
Function and homology information


membrane disassembly / regulation of adipose tissue development / ether lipid metabolic process / phosphatidylethanolamine acyl-chain remodeling / organelle disassembly / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS ...membrane disassembly / regulation of adipose tissue development / ether lipid metabolic process / phosphatidylethanolamine acyl-chain remodeling / organelle disassembly / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / phospholipase A1 activity / peroxisome organization / N-acyltransferase activity / phospholipase A2 activity / lens fiber cell differentiation / phospholipid biosynthetic process / phospholipase A2 / peroxisomal membrane / triglyceride metabolic process / acyltransferase activity / lipid catabolic process / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to bacterium / mitochondrial membrane / peroxisome / nuclear envelope / lysosome / lysosomal membrane / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Lecithin retinol acyltransferase / LRAT domain / LRAT domain profile. / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phospholipase A and acyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsRen, X. / Xia, B.
CitationJournal: Febs Lett. / Year: 2010
Title: Solution structure of the N-terminal catalytic domain of human H-REV107--a novel circular permutated NlpC/P60 domain
Authors: Ren, X. / Lin, J. / Jin, C. / Xia, B.
History
DepositionJun 8, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group XVI phospholipase A2


Theoretical massNumber of molelcules
Total (without water)13,9671
Polymers13,9671
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Group XVI phospholipase A2 / Adipose-specific phospholipase A2 / AdPLA / HRAS-like suppressor 3 / H-rev 107 protein homolog / ...Adipose-specific phospholipase A2 / AdPLA / HRAS-like suppressor 3 / H-rev 107 protein homolog / HREV107-3 / Renal carcinoma antigen NY-REN-65


Mass: 13966.923 Da / Num. of mol.: 1 / Fragment: UNP residues 1-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G16, HRASLS3, HREV107 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53816, phospholipase A2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D (H)CCH-TOCSY
1713D HBHA(CO)NH
1813D (H)CCH-COSY
1913D (H)CCH-COSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] H-REV107N-1, 30 mM sodium phosphate-2, 30 mM sodium chloride-3, 10 mM DTT-4, 90 % H2O-5, 10 % D2O-6, 0.05 w/v sodium azide-7, 0.02 w/v DSS-8, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMH-REV107N-1[U-13C; U-15N]1
30 mMsodium phosphate-21
30 mMsodium chloride-31
10 mMDTT-41
90 %H2O-51
10 %D2O-61
0.05 w/vsodium azide-71
0.02 w/vDSS-81
Sample conditionsIonic strength: 60 / pH: 7 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificdata analysis
XwinNMR3.5Bruker Biospincollection
TopSpin2.1Bruker Biospincollection
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
CYANAGuntert, Mumenthaler and Wuthrichstruture calculation
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstruture calculation
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
ProcheckNMRLaskowski and MacArthurstructure analysis
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3484 / NOE intraresidue total count: 1317 / NOE long range total count: 543 / NOE medium range total count: 315 / NOE sequential total count: 655
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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