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- PDB-1kuw: High-Resolution Structure and Localization of Amylin Nucleation S... -

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Basic information

Entry
Database: PDB / ID: 1kuw
TitleHigh-Resolution Structure and Localization of Amylin Nucleation Site in Detergent Micelles
ComponentsIslet amyloid polypeptideAmylin
KeywordsHORMONE/GROWTH FACTOR / amylin / hIAPP / micelles / orientation / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / positive regulation of cAMP-mediated signaling ...: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / positive regulation of cAMP-mediated signaling / negative regulation of protein-containing complex assembly / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
Islet amyloid polypeptide
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsMascioni, A. / Porcelli, F. / Ilangovan, U. / Ramamoorthy, A. / Veglia, G.
CitationJournal: Biopolymers / Year: 2003
Title: Conformational preferences of the amylin nucleation site in SDS micelles: an NMR study.
Authors: Mascioni, A. / Porcelli, F. / Ilangovan, U. / Ramamoorthy, A. / Veglia, G.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)1,0091
Polymers1,0091
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)39 / 100structures with the lowest energy
RepresentativeModel #6

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Components

#1: Protein/peptide Islet amyloid polypeptide / Amylin / Amylin


Mass: 1009.073 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS.
References: UniProt: P10997

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D-TOCSY

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Sample preparation

DetailsContents: 20mM PBS buffer, 100mM d25-SDS / Solvent system: water
Sample conditionspH: 4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
Sparky1.1Gottarddata analysis
NMRPipe1.1Delaglioprocessing
X-PLOR3.851Brunger et. al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 39

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