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- PDB-8ani: Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown ... -

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Basic information

Entry
Database: PDB / ID: 8ani
TitleStructure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 10% ethanol
ComponentsPeptide LYIQWL from Tc5b
KeywordsPROTEIN FIBRIL / amyloid
Function / homologyETHANOL / trifluoroacetic acid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide LYIQWL from Tc5b
B: Peptide LYIQWL from Tc5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8765
Polymers1,6702
Non-polymers2063
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: ECD measurements confirmed amyloid formation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)11.719, 23.467, 18.762
Angle α, β, γ (deg.)90.000, 90.040, 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 LYIQWL from Tc5b


Mass: 835.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.54 Å3/Da / Density % sol: 20.38 %
Crystal growTemperature: 293 K / Method: evaporation, recrystallization
Details: Peptide was dissolved in 10% ethanol at 0.5 mg/ml concentration, then incubated at 293K overnight.

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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: Jan 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.35→18.76 Å / Num. obs: 2253 / % possible obs: 98.13 % / Redundancy: 4.93 % / Biso Wilson estimate: 5.6 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.168 / Net I/σ(I): 7
Reflection shellResolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 214 / CC1/2: 0.756 / Rrim(I) all: 0.745

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: crystal structure of LYIQWL grown from acetonitrile/water

Resolution: 1.35→18.76 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.6422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1522 221 9.85 %
Rwork0.1142 2023 -
obs0.1177 2244 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.95 Å2
Refinement stepCycle: LAST / Resolution: 1.35→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms120 0 13 3 136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128150
X-RAY DIFFRACTIONf_angle_d1.4097202
X-RAY DIFFRACTIONf_chiral_restr0.111220
X-RAY DIFFRACTIONf_plane_restr0.008621
X-RAY DIFFRACTIONf_dihedral_angle_d14.974445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.70.20641100.1433995X-RAY DIFFRACTION96.34
1.7-18.760.12791110.10131028X-RAY DIFFRACTION99.13
Refinement TLS params.Method: refined / Origin x: -0.607611122042 Å / Origin y: 0.80800839191 Å / Origin z: 1.79779049102 Å
111213212223313233
T0.0288371400041 Å20.00198204976032 Å2-0.0115577499744 Å2-0.0502413523014 Å20.00361905222268 Å2--0.0389507047865 Å2
L0.91532962831 °2-0.0944160974928 °2-0.331591182629 °2-1.12936386253 °20.792861941234 °2--1.67857714863 °2
S0.0125582259765 Å °-0.0060301564509 Å °-0.0132532061162 Å °-0.0363810737111 Å °0.00994568756375 Å °0.00763677821185 Å °-0.0216989752144 Å °-0.0324529579734 Å °-0.0241734553911 Å °
Refinement TLS groupSelection details: all

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