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- PDB-1n2y: SOLUTION STRUCTURE OF SS-CYCLIZED CATESTATIN FRAGMENT FROM CHROMO... -

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Basic information

Entry
Database: PDB / ID: 1n2y
TitleSOLUTION STRUCTURE OF SS-CYCLIZED CATESTATIN FRAGMENT FROM CHROMOGRANIN A
ComponentsCATESTATIN
KeywordsSIGNALING PROTEIN / CATESTATIN CHOROMOGRANIN A
Function / homology
Function and homology information


: / mast cell cytokine production / adenylate cyclase-activating adrenergic receptor signaling pathway involved in cardiac muscle relaxation / negative regulation of catecholamine secretion / negative regulation of protein serine/threonine phosphatase activity / positive regulation of dense core granule biogenesis / mast cell granule / mast cell chemotaxis / mast cell activation / negative regulation of hormone secretion ...: / mast cell cytokine production / adenylate cyclase-activating adrenergic receptor signaling pathway involved in cardiac muscle relaxation / negative regulation of catecholamine secretion / negative regulation of protein serine/threonine phosphatase activity / positive regulation of dense core granule biogenesis / mast cell granule / mast cell chemotaxis / mast cell activation / negative regulation of hormone secretion / chromaffin granule / antifungal humoral response / mast cell degranulation / neuronal dense core vesicle / negative regulation of insulin secretion / defense response to fungus / regulation of cell adhesion / transport vesicle / negative regulation of angiogenesis / secretory granule / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / calcium ion binding / extracellular space / extracellular region
Similarity search - Function
Chromogranin A/B / Chromogranin A/B/C / Chromogranin, conserved site / Granin (chromogranin or secretogranin) / Granins signature 1. / Granins signature 2.
Similarity search - Domain/homology
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, CHEMICAL SHIFT REFINEMENT
AuthorsPreece, N.E. / Nguyen, M. / Mahata, M. / Mahata, S.K. / Mahapatra, N.R. / Tsigelny, I. / O'Connor, D.T.
CitationJournal: Regul.Pept. / Year: 2004
Title: Conformational preferences and activities of peptides from the catecholamine release-inhibitory (catestatin) region of chromogranin A
Authors: Preece, N.E. / Nguyen, M. / Mahata, M. / Mahata, S.K. / Mahapatra, N.R. / Tsigelny, I. / O'Connor, D.T.
History
DepositionOct 24, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 13, 2002ID: 1krk
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999SEQUENCE THE TERMINAL CYSTEINES ARE NON-NATIVE BUT WERE INCLUDED TO FACILITATE THE SYNTHESIS OF THE ...SEQUENCE THE TERMINAL CYSTEINES ARE NON-NATIVE BUT WERE INCLUDED TO FACILITATE THE SYNTHESIS OF THE CYCLIC PEPTIDE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATESTATIN


Theoretical massNumber of molelcules
Total (without water)1,6631
Polymers1,6631
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)12 / 20DOMINANT CLUSTER and outliers
RepresentativeModel #8

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Components

#1: Protein/peptide CATESTATIN


Mass: 1662.961 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. SOLID PHASE SYNTHESIS AND FACILE CYCLIZATION OF TERMINAL CYSTEINES BY OXIDATION WAS PERFORMED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN BOS TAURUS (COW).
References: UniProt: P05059

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131P-COSY
141BASHD-TOCSY
NMR detailsText: DMSO-D6

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Sample preparation

DetailsContents: 4MG SS-CYCLIZED CATESTATIN 15-MER
Sample conditionsIonic strength: 10 mM PHOSPHATE / pH: 7 / Pressure: AMBIENT / Temperature: 278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameClassification
X-PLORrefinement
VNMRstructure solution
Felixstructure solution
Discoverstructure solution
X-PLORstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, CHEMICAL SHIFT REFINEMENT
Software ordinal: 1
NMR ensembleConformer selection criteria: DOMINANT CLUSTER and outliers / Conformers calculated total number: 20 / Conformers submitted total number: 12

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