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- PDB-8anj: Structure of the amyloid-forming peptide DFINWL from human GLP-2 -

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Basic information

Entry
Database: PDB / ID: 8anj
TitleStructure of the amyloid-forming peptide DFINWL from human GLP-2
ComponentsPeptide DFINWL from human GLP-2
KeywordsPROTEIN FIBRIL / amyloid
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Peptide DFINWL from human GLP-2


Theoretical massNumber of molelcules
Total (without water)8071
Polymers8071
Non-polymers00
Water181
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 area1080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.780, 4.869, 21.936
Angle α, β, γ (deg.)90.000, 101.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide Peptide DFINWL from human GLP-2


Mass: 806.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 310 K / Method: evaporation, recrystallization
Details: Lyophilized peptide was dissolved in 0.6 mg/ml concentration in a solution containing 30 % acetonitrile and 0.1 % TFA and incubated at 310K for 4 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: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.55→16.96 Å / Num. obs: 773 / % possible obs: 98.35 % / Redundancy: 2.88 % / Biso Wilson estimate: 12.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.067 / Net I/σ(I): 12.1
Reflection shellResolution: 1.55→1.61 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 77 / CC1/2: 0.921 / Rrim(I) all: 0.356 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: crystal structure of LYIQWL

Resolution: 1.55→16.95 Å / SU ML: 0.0963 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.2751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1744 74 9.64 %
Rwork0.1683 694 -
obs0.1689 768 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.34 Å2
Refinement stepCycle: LAST / Resolution: 1.55→16.95 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms58 0 0 1 59
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01160
X-RAY DIFFRACTIONf_angle_d0.955982
X-RAY DIFFRACTIONf_chiral_restr0.06718
X-RAY DIFFRACTIONf_plane_restr0.007510
X-RAY DIFFRACTIONf_dihedral_angle_d8.850918
LS refinement shellResolution: 1.55→16.95 Å
RfactorNum. reflection% reflection
Rfree0.1744 74 -
Rwork0.1683 694 -
obs--97.71 %

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