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- PDB-5k5g: Structure of human islet amyloid polypeptide in complex with an e... -

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Basic information

Entry
Database: PDB / ID: 5k5g
TitleStructure of human islet amyloid polypeptide in complex with an engineered binding protein
Components
  • HI18
  • Islet amyloid polypeptideAmylin
KeywordsHORMONE / amyloid / type 2 diabetes / beta-hairpin / signaling protein
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 cAMP-mediated signaling / 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 / Immunoglobulin FC, subunit C / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Immunoglobulin FC, subunit C / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Islet amyloid polypeptide
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMirecka, E.A. / Feuerstein, S. / Gremer, L. / Schroeder, G.F. / Stoldt, M. / Willbold, D. / Hoyer, W.
CitationJournal: Sci Rep / Year: 2016
Title: beta-Hairpin of Islet Amyloid Polypeptide Bound to an Aggregation Inhibitor.
Authors: Mirecka, E.A. / Feuerstein, S. / Gremer, L. / Schroder, G.F. / Stoldt, M. / Willbold, D. / Hoyer, W.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection
Category: pdbx_database_PDB_obs_spr / pdbx_database_proc / pdbx_nmr_software
Item: _pdbx_nmr_software.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Mar 8, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Islet amyloid polypeptide
B: HI18
C: HI18


Theoretical massNumber of molelcules
Total (without water)19,5193
Polymers19,5193
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area6040 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide Islet amyloid polypeptide / Amylin / 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) / Cell: B-CELL / Gene: IAPP / Organ: PANCREAS / Plasmid: PET302 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10997
#2: Protein HI18


Mass: 7804.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PET302 / Production host: Escherichia coli BL21(DE3) (bacteria)

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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 HNCA
131isotropic13D HNHA
141isotropic13D HN(CA)CB
151isotropic13D 1H-15N NOESY
161isotropic13D HNCO
171isotropic13D (H)CCH-COSY
181isotropic13D 1H-13C NOESY
192isotropic22D 1H-15N HSQC
1102isotropic23D HNCA
1112isotropic23D HNHA
1122isotropic23D HN(CA)CB
1132isotropic23D 1H-15N NOESY
1142isotropic23D (H)CCH-COSY
1152isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.40 mM [U-13C; U-15N] ISLET AMYLOID POLYPEPTIDE, 0.48 mM HI18, 20 mM sodium phosphate, 93% H2O/7% D2O13C-15N-IAPP, NA-HI1813C_15N_IAPP93% H2O/7% D2O
solution20.48 mM ISLET AMYLOID POLYPEPTIDE, 0.40 mM [U-13C; U-15N] HI18, 20 mM sodium phosphate, 93% H2O/7% D2ONA-IAPP, 13C-15N-HI1813C_15N_HI1893% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.40 mMISLET AMYLOID POLYPEPTIDE[U-13C; U-15N]1
0.48 mMHI18natural abundance1
20 mMsodium phosphatenatural abundance1
0.48 mMISLET AMYLOID POLYPEPTIDEnatural abundance2
0.40 mMHI18[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNMRSVarianVNMRS9002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21BRUNGER A. T. ET.AL.refinement
ARIA2.3.2LINGErefinement
CcpNmr Analysis2.3structure solution
NMRPipe7.9structure solution
VnmrJ2.3Astructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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