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- PDB-5mgq: Solution structure of oxidized and amidated human IAPP (1-37), th... -

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Basic information

Entry
Database: PDB / ID: 5mgq
TitleSolution structure of oxidized and amidated human IAPP (1-37), the diabetes II peptide.
ComponentsIslet amyloid polypeptide
KeywordsPROTEIN FIBRIL / Recombinant human IAPP / Type II Diabetes
Function / homology
Function and homology information


amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / 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 / Regulation of gene expression in beta cells ...amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / 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 / Regulation of gene expression in beta cells / positive regulation of cAMP/PKA signal transduction / bone resorption / negative regulation of protein-containing complex assembly / 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 / positive regulation of apoptotic process / Amyloid fiber formation / receptor ligand activity / signaling receptor binding / neuronal cell body / 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 / molecular dynamics
AuthorsRodriguez Camargo, D.C. / Tripsianes, K. / Reif, B.
Funding support Germany, Czech Republic, 3items
OrganizationGrant numberCountry
German Research FoundationProject-B07 Germany
Helmholtz-GemeinschaftGrants Re1435 Germany
Ministry of Education, Youth and Sports of the Czech RepublicCEITEC 2020 (LQ1601) Czech Republic
CitationJournal: Sci Rep / Year: 2017
Title: The redox environment triggers conformational changes and aggregation of hIAPP in Type II Diabetes.
Authors: Rodriguez Camargo, D.C. / Tripsianes, K. / Buday, K. / Franko, A. / Gobl, C. / Hartlmuller, C. / Sarkar, R. / Aichler, M. / Mettenleiter, G. / Schulz, M. / Boddrich, A. / Erck, C. / Martens, ...Authors: Rodriguez Camargo, D.C. / Tripsianes, K. / Buday, K. / Franko, A. / Gobl, C. / Hartlmuller, C. / Sarkar, R. / Aichler, M. / Mettenleiter, G. / Schulz, M. / Boddrich, A. / Erck, C. / Martens, H. / Walch, A.K. / Madl, T. / Wanker, E.E. / Conrad, M. / de Angelis, M.H. / Reif, B.
History
DepositionNov 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Structure summary / Category: entity / Item: _entity.details
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0Apr 9, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)3,9071
Polymers3,9071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area3260 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Islet amyloid polypeptide


Mass: 3907.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue name "TYC" refers to amidation of C-terminal TYR.
Source: (gene. exp.) Homo sapiens (human) / Gene: IAPP
Details (production host): Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.
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
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic23D (H)CCH-TOCSY
161isotropic33D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 150 uM [U-99% 13C; U-99% 15N] Islet Amyloid Polypeptide (IAPP or Amylin), 90% H2O/10% D2O
Label: 15_N13_C hIAPP / Solvent system: 90% H2O/10% D2O
SampleConc.: 150 uM / Component: Islet Amyloid Polypeptide (IAPP or Amylin) / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: Lyophilized hIAPP(1-37) was dissolved into NMR buffer (30 mM deuterated acetic acid, pH 5.3) containing 10 % D2O for locking. The samples were measured and stored at 277K. The formation of ...Details: Lyophilized hIAPP(1-37) was dissolved into NMR buffer (30 mM deuterated acetic acid, pH 5.3) containing 10 % D2O for locking. The samples were measured and stored at 277K. The formation of the intramolecular disulfide bond was confirmed by NMR
Ionic strength: 0 Not defined / Label: 15_N13_C hIAPP / pH: 5.3 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7503

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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