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- PDB-2kb8: The dynamic alpha-helix structure of micelle-bound human amylin. -

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Basic information

Entry
Database: PDB / ID: 2kb8
TitleThe dynamic alpha-helix structure of micelle-bound human amylin.
ComponentsIslet amyloid polypeptide
KeywordsHORMONE / IAPP / amyloid / Micelle-bound / type II diabetes / Amidation / Cleavage on pair of basic residues / Polymorphism / Secreted
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 / negative regulation of protein-containing complex assembly ...: / 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 / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsPatil, S.M. / Xu, S. / Sheftic, S.R. / Alexandrescu, A.T.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Dynamic alpha-helix structure of micelle-bound human amylin.
Authors: Patil, S.M. / Xu, S. / Sheftic, S.R. / Alexandrescu, A.T.
History
DepositionNov 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)3,9091
Polymers3,9091
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)30 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Islet amyloid polypeptide / Amylin / Diabetes-associated peptide / DAP / Insulinoma amyloid peptide


Mass: 3909.304 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Recombinant 15N-labeled amylin was purchased from rPeptide
Gene: IAPP / Production host: Escherichia coli (E. coli) / References: UniProt: P10997

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1223D HNCA
1323D HNHB
1422D 1H-1H NOESY
1523D TROSY
1623D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] amylin, 100 mM [U-99% 2H] sodium dodecyl sulfate, 60 mM [U-99% 2H] acetic acid, 100% D2O100% D2O
20.5 mM [U-99% 15N] amylin, 100 mM [U-2H] SDS, 60 mM acetic acid, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMamylin[U-100% 15N]1
100 mMsodium dodecyl sulfate[U-99% 2H]1
60 mMacetic acid[U-99% 2H]1
0.5 mMamylin[U-99% 15N]2
100 mMSDS[U-2H]2
60 mMacetic acid2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
160 4.6 ambient 310 K
260 310 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsHydrogen bond constraints total count: 34 / Protein chi angle constraints total count: 8 / Protein phi angle constraints total count: 22
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 30

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