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- PDB-6ucj: proIAPP in DPC Micelles - Two-Conformer Ensemble Refinement, Open... -

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Open data


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Basic information

Entry
Database: PDB / ID: 6ucj
TitleproIAPP in DPC Micelles - Two-Conformer Ensemble Refinement, Open Conformer
ComponentsIslet amyloid polypeptide
KeywordsHORMONE / membrane-binding / IDP / amyloid
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 / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / bone resorption ...amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / bone resorption / sensory perception of pain / positive regulation of calcium-mediated signaling / 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 / simulated annealing
AuthorsDeLisle, C.F. / Malooley, A.L. / Banerjee, I. / Lorieau, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1651598 United States
CitationJournal: Febs J. / Year: 2020
Title: Pro-islet amyloid polypeptide in micelles contains a helical prohormone segment.
Authors: DeLisle, C.F. / Malooley, A.L. / Banerjee, I. / Lorieau, J.L.
History
DepositionSep 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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)8,0451
Polymers8,0451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: 15N relaxation supports a tumbling time representative of monomeric proIAPP bound to one micelle
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 800structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 8045.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta / Gene: IAPP / Organ: Pancreas / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10997
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
162isotropic13D 1H-15N NOESY
171isotropic23D (H)CCH-TOCSY
181anisotropic12D 1H-15N IPAP-HSQC
191anisotropic13D H-HCACO

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle11.0 mM [U-13C; U-15N] CN-proIAPP-K4D, 200 mM DPC, 30 mM sodium acetate, 50 mM sodium chloride, 0.03 % w/w sodium azide, 90% H2O/10% D2OFor backbone / side-chain assignmentCN-proIAPP-K4D90% H2O/10% D2O
micelle21.0 mM [U-15N] N-proIAPP-K4D, 200 mM [U-100% 2H] DPC, 30 mM sodium acetate, 50 mM sodium chloride, 0.03 % w/w sodium azide, 90% H2O/10% D2OFor NOE collectionN-proIAPP-K4D90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMCN-proIAPP-K4D[U-13C; U-15N]1
200 mMDPCnatural abundance1
30 mMsodium acetatenatural abundance1
50 mMsodium chloridenatural abundance1
0.03 % w/wsodium azidenatural abundance1
1.0 mMN-proIAPP-K4D[U-15N]2
200 mMDPC[U-100% 2H]2
30 mMsodium acetatenatural abundance2
50 mMsodium chloridenatural abundance2
0.03 % w/wsodium azidenatural abundance2
Sample conditionsIonic strength: 50 mM NaCl mM / Label: condition_1 / pH: 4.5 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinal
simulated annealing1
simulated annealing2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 800 / Conformers submitted total number: 20

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