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- PDB-6nzn: Dimer-of-dimer amyloid fibril structure of glucagon -

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Basic information

Entry
Database: PDB / ID: 6nzn
TitleDimer-of-dimer amyloid fibril structure of glucagon
ComponentsGlucagon
KeywordsHORMONE / PROTEIN FIBRIL / amyloid
Function / homology
Function and homology information


glucagon receptor binding / protein kinase A signaling / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / regulation of insulin secretion / cellular response to glucagon stimulus ...glucagon receptor binding / protein kinase A signaling / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / regulation of insulin secretion / cellular response to glucagon stimulus / response to activity / gluconeogenesis / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / secretory granule lumen / G alpha (s) signalling events / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsGelenter, M.D. / Smith, K.J. / Liao, S.Y. / Mandala, V.S. / Dregni, A.J. / Lamm, M.S. / Tian, Y. / Wei, X. / Pochan, D.J. / Tucker, T.J. ...Gelenter, M.D. / Smith, K.J. / Liao, S.Y. / Mandala, V.S. / Dregni, A.J. / Lamm, M.S. / Tian, Y. / Wei, X. / Pochan, D.J. / Tucker, T.J. / Su, Y. / Hong, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI133989 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: The peptide hormone glucagon forms amyloid fibrils with two coexisting beta-strand conformations.
Authors: Gelenter, M.D. / Smith, K.J. / Liao, S.Y. / Mandala, V.S. / Dregni, A.J. / Lamm, M.S. / Tian, Y. / Xu, W. / Pochan, D.J. / Tucker, T.J. / Su, Y. / Hong, M.
History
DepositionFeb 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Advisory / Database references / Other
Category: database_2 / pdbx_database_remark / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucagon
B: Glucagon
C: Glucagon
D: Glucagon
E: Glucagon
F: Glucagon
G: Glucagon
H: Glucagon
I: Glucagon
J: Glucagon
K: Glucagon
L: Glucagon
M: Glucagon
N: Glucagon
O: Glucagon
P: Glucagon


Theoretical massNumber of molelcules
Total (without water)55,78816
Polymers55,78816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44590 Å2
ΔGint-130 kcal/mol
Surface area22610 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 700target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide
Glucagon


Mass: 3486.781 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 13C-13C CORD
1101isotropic12D 15N-13C NCA
122isotropic22D 13C-13C CORD
1112isotropic12D 13C-13C CORD
162isotropic12D 15N-13C NCCX
174isotropic13D 15N-13C-13C NCCX
1134isotropic12D 13C-13C CORD
1144isotropic22D-13C-13C CORD
183isotropic33D 15N-13C-13C NCACX
193isotropic33D 15N-13C-13C NCOCX
1153isotropic12D 13C-13C CORD
1163isotropic22D 13C-13C PDSD
132isotropic22D 15N-13C PERSPIRATION-CP
142isotropic22D 13C-13C PAR
152isotropic12D CHHC
1124isotropic12D CHHC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
fibrous protein10.1 mg/uL {U-13C; U-15N]-G4,S8,L14,A19,V23 Glucagon, water1water
fibrous protein20.1 mg/uL {U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28 Glucagon, water7cwater
fibrous protein30.1 mg/uL {U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24 Glucagon, water8cwater
fibrous protein40.1 mg/uL {U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19 Glucagon, water9cwater
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mg/uLGlucagon{U-13C; U-15N]-G4,S8,L14,A19,V231
0.1 mg/uLGlucagon{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N282
0.1 mg/uLGlucagon{U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q243
0.1 mg/uLGlucagon{U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A194
Sample conditionsIonic strength: 0.01 M / Ionic strength err: 0.002 / Label: 1 / pH: 2 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 293 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE III HDBrukerAVANCE III HD6002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
SparkyNMRFAM-SPARKY 1.412Goddardchemical shift assignment
TopSpin3.5Bruker Biospinprocessing
SparkyNMRFAM-SPARKY 1.412Goddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 700 / Conformers submitted total number: 10

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