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- PDB-8ank: Structure of the amyloid-forming peptide pEFIAWL from human GLP-1 -

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Basic information

Entry
Database: PDB / ID: 8ank
TitleStructure of the amyloid-forming peptide pEFIAWL from human GLP-1
ComponentsPeptide pEFIAWL from hGLP-1
KeywordsPROTEIN FIBRIL / amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDurvanger, Z.
Funding support Hungary, European Union, 3items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
European Regional Development FundVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation OfficeThematic Excellence Program Synth+ Hungary
CitationJournal: Nat Commun / Year: 2023
Title: Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation.
Authors: Horvath, D. / Durvanger, Z. / K Menyhard, D. / Sulyok-Eiler, M. / Bencs, F. / Gyulai, G. / Horvath, P. / Taricska, N. / Perczel, A.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: 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
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide pEFIAWL from hGLP-1


Theoretical massNumber of molelcules
Total (without water)7601
Polymers7601
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: ECD measurements confirmed amyloid formation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.710, 9.545, 22.396
Angle α, β, γ (deg.)90.000, 92.740, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

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Components

#1: Protein/peptide Peptide pEFIAWL from hGLP-1


Mass: 759.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.45 Å3/Da / Density % sol: 15.46 %
Crystal growTemperature: 310 K / Method: evaporation, recrystallization
Details: EFIAWL was dissolved in 0.15 - 0.5 mg/ml concentration in a solution containing 30 % acetonitrile and 0.1 % TFA and incubated at 310K for several weeks.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.3→11.19 Å / Num. obs: 1157 / % possible obs: 99.83 % / Redundancy: 4.78 % / Biso Wilson estimate: 5.48 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.106 / Net I/σ(I): 13.6
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 114 / CC1/2: 0.893 / Rrim(I) all: 0.331 / % possible all: 99.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
Fragonphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal 5 residue beta strand form the software Fragon

Resolution: 1.3→11.19 Å / SU ML: 0.0624 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 10.9139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1298 121 10.49 %
Rwork0.1013 1032 -
obs0.1039 1153 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.34 Å2
Refinement stepCycle: LAST / Resolution: 1.3→11.19 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms55 0 0 2 57
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014658
X-RAY DIFFRACTIONf_angle_d1.910880
X-RAY DIFFRACTIONf_chiral_restr0.11168
X-RAY DIFFRACTIONf_plane_restr0.0099
X-RAY DIFFRACTIONf_dihedral_angle_d22.717218
LS refinement shellResolution: 1.3→11.19 Å
RfactorNum. reflection% reflection
Rfree0.1298 121 -
Rwork0.1013 1032 -
obs--99.48 %

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