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- PDB-8ddg: FYF peptide forms a standard beta-sheet -

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Basic information

Entry
Database: PDB / ID: 8ddg
TitleFYF peptide forms a standard beta-sheet
ComponentsPHE-TYR-PHE
KeywordsPROTEIN FIBRIL / Rippled beta-sheet / Racemic peptide
Biological speciessynthetic construct (others)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / FOURIER SYNTHESIS / Resolution: 0.9 Å
AuthorsSawaya, M.R. / Hazari, A. / Eisenberg, D.E. / Vlahakis, N.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2022
Title: The rippled β-sheet layer configuration-a novel supramolecular architecture based on predictions by Pauling and Corey.
Authors: Amaruka Hazari / Michael R Sawaya / Niko Vlahakis / Timothy C Johnstone / David Boyer / Jose Rodriguez / David Eisenberg / Jevgenij A Raskatov /
Abstract: The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since ...The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since observed in countless proteins and peptides and is considered common textbook knowledge. Conversely, the rippled β-sheet only gained a meaningful experimental foundation in the past decade, and the first crystal structural study of rippled β-sheets was published as recently as this year. Noteworthy, the crystallized assembly stopped at the rippled β-dimer stage. It did not form the extended, periodic rippled β-sheet layer topography hypothesized by Pauling and Corey, thus calling the validity of their prediction into question. NMR work conducted since moreover shows that certain model peptides rather form pleated and not rippled β-sheets in solution. To determine whether the periodic rippled β-sheet layer configuration is viable, the field urgently needs crystal structures. Here we report on crystal structures of two racemic and one quasi-racemic aggregating peptide systems, all of which yield periodic rippled antiparallel β-sheet layers that are in excellent agreement with the predictions by Pauling and Corey. Our study establishes the rippled β-sheet layer configuration as a motif with general features and opens the road to structure-based design of unique supramolecular architectures.
History
DepositionJun 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 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: PHE-TYR-PHE


Theoretical massNumber of molelcules
Total (without water)4761
Polymers4761
Non-polymers00
Water0
1
A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE

A: PHE-TYR-PHE


Theoretical massNumber of molelcules
Total (without water)2,3785
Polymers2,3785
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_575x,y+2,z1
Unit cell
Length a, b, c (Å)23.140, 4.840, 19.790
Angle α, β, γ (deg.)90.000, 107.048, 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

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Components

#1: Protein/peptide PHE-TYR-PHE


Mass: 475.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: FYF peptide / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: unidentified (others)
Source (recombinant)Organism: unidentified (others)
Buffer solutionpH: 4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO / Details: crystal

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Data collection

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 5000 nm
Image recordingAverage exposure time: 3 sec. / Electron dose: 0.0192 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM diffractionCamera length: 1320 mm
EM diffraction shellResolution: 0.9→1 Å / Fourier space coverage: 72.2 % / Multiplicity: 4.9 / Num. of structure factors: 332 / Phase residual: 13.5 °
EM diffraction statsFourier space coverage: 71 % / High resolution: 0.9 Å / Num. of intensities measured: 5980 / Num. of structure factors: 1237 / Phase error rejection criteria: 20 / Rmerge: 0.113
Diffraction sourceSource: ELECTRON MICROSCOPE / Wavelength: 0.0197 Å
DetectorType: TVIPS TEMCAM-F416 / Detector: POSITION SENSITIVE DETECTOR / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0197 Å / Relative weight: 1
ReflectionResolution: 0.9→18.92 Å / Num. obs: 1237 / % possible obs: 71 % / Redundancy: 4.834 % / Biso Wilson estimate: 6.869 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.129 / Χ2: 0.932 / Net I/σ(I): 8.63 / Num. measured all: 5980 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.9-14.9370.3225.0116394603320.6430.36672.2
1-1.14.940.181710773022180.9630.20572.2
1.1-1.24.9770.1538.958662261740.9850.17377
1.2-1.54.8330.1489.5111893452460.9730.16871.3
1.5-24.7240.09112.957182261520.9870.10467.3
2-2.34.810.09714.9320262420.990.10967.7
2.3-34.0830.08313.2614759360.9950.09461
3-53.9410.07213.9413450340.9930.08568
5-82.6670.03413.0686310.04750

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.27data extraction
SHELXDphasing
EM 3D crystal entity∠α: 90 ° / ∠β: 107.05 ° / ∠γ: 90 ° / A: 23.14 Å / B: 4.84 Å / C: 19.79 Å / Space group name: C2 / Space group num: 5
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.9→5.78 Å / SU ML: 0.0753 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.6089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1851 112 9.09 %
Rwork0.1692 1120 -
obs0.1704 1232 71.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 3.26 Å2
Refinement stepCycle: LAST / Resolution: 0.9→5.78 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms35 0 0 0 35
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0237
ELECTRON CRYSTALLOGRAPHYf_angle_d1.253649
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.09033
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00786
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d19.20064
LS refinement shellResolution: 0.9→5.78 Å
RfactorNum. reflection% reflection
Rfree0.1851 112 -
Rwork0.1692 1120 -
obs--71.21 %

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