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- PDB-6wky: Cryo-EM of Form 1 related peptide filament, 29-24-3 -

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Database: PDB / ID: 6wky
TitleCryo-EM of Form 1 related peptide filament, 29-24-3
Componentspeptide 29-24-3
KeywordsPROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, F. / Gnewou, O.M. / Egelman, E.H. / Conticello, V.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
CitationJournal: To Be Published
Title: Cryo-EM of Form 1 related peptide filament, 29-24-3
Authors: Wang, F. / Gnewou, O.M. / Egelman, E.H. / Conticello, V.P.
Validation Report
SummaryFull reportAbout validation report
DepositionApr 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release

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Deposited unit
B: peptide 29-24-3
C: peptide 29-24-3
D: peptide 29-24-3
A: peptide 29-24-3
E: peptide 29-24-3
F: peptide 29-24-3
G: peptide 29-24-3
H: peptide 29-24-3
I: peptide 29-24-3
J: peptide 29-24-3
K: peptide 29-24-3
L: peptide 29-24-3
M: peptide 29-24-3
N: peptide 29-24-3
O: peptide 29-24-3
P: peptide 29-24-3
Q: peptide 29-24-3
R: peptide 29-24-3
S: peptide 29-24-3
T: peptide 29-24-3
a: peptide 29-24-3
b: peptide 29-24-3
c: peptide 29-24-3
d: peptide 29-24-3
e: peptide 29-24-3
f: peptide 29-24-3
g: peptide 29-24-3
h: peptide 29-24-3
i: peptide 29-24-3
j: peptide 29-24-3
k: peptide 29-24-3
l: peptide 29-24-3
m: peptide 29-24-3
n: peptide 29-24-3
o: peptide 29-24-3
p: peptide 29-24-3
q: peptide 29-24-3
r: peptide 29-24-3
s: peptide 29-24-3
t: peptide 29-24-3

Theoretical massNumber of molelcules
Total (without water)130,15140

  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area69200 Å2
ΔGint-379 kcal/mol
Surface area51370 Å2
SymmetryHelical symmetry: (Circular symmetry: 4 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 40 / Rise per n subunits: 7.96 Å / Rotation per n subunits: 10.88 °)


#1: Protein/peptide ...
peptide 29-24-3

Mass: 3253.769 Da / Num. of mol.: 40 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

Experimental details


EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

Sample preparation

ComponentName: self-assembly peptide filament, 29-24-3 / Type: COMPLEX / Details: synthetic peptide / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
Helical symmertyAngular rotation/subunit: 10.88 ° / Axial rise/subunit: 7.96 Å / Axial symmetry: C4
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 12869 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL

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