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- PDB-2kj7: Three-Dimensional NMR Structure of Rat Islet Amyloid Polypeptide ... -

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Basic information

Entry
Database: PDB / ID: 2kj7
TitleThree-Dimensional NMR Structure of Rat Islet Amyloid Polypeptide in DPC micelles
ComponentsIslet amyloid polypeptideAmylin
KeywordsHORMONE / IAPP / Amylin / Islet Amyloid Polypeptide / Rat IAPP / Amidation / Amyloid / Cleavage on pair of basic residues / Disulfide bond / Secreted
Function / homology
Function and homology information


Calcitonin-like ligand receptors / amylin receptor signaling pathway / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / positive regulation of cAMP-mediated signaling / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain ...Calcitonin-like ligand receptors / amylin receptor signaling pathway / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / positive regulation of cAMP-mediated signaling / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain / osteoclast differentiation / secretory granule / hormone activity / glucose metabolic process / receptor ligand activity / signaling receptor binding / neuronal cell body / lipid binding / extracellular space / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsfewest violations, model 1
AuthorsNanga, R. / Brender, J.R. / Xu, J. / Hartman, K. / Subramanian, V. / Ramamoorthy, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Three-dimensional structure and orientation of rat islet amyloid polypeptide protein in a membrane environment by solution NMR spectroscopy.
Authors: Nanga, R.P. / Brender, J.R. / Xu, J. / Hartman, K. / Subramanian, V. / Ramamoorthy, A.
History
DepositionMay 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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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)3,9241
Polymers3,9241
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)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 3924.426 Da / Num. of mol.: 1 / Fragment: Rat IAPP, UNP residues 38-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Iapp / References: UniProt: P12969

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 20 mM sodium phosphate, 0.02 % sodium azide, 120 mM sodium chloride, 10 % 99.9% D2O, 200 mM 98% deuterated DPC, 2.5 mM entity, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
0.02 %sodium azide-21
120 mMsodium chloride-31
10 %D2O-499.9%1
200 mMDPC-598% deuterated1
2.5 mMentity-61
Sample conditionsIonic strength: 120 / pH: 7.3 / Pressure: ambient atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddardchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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