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- PDB-6wl8: Cryo-EM of Form 2 peptide filament -

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Basic information

Entry
Database: PDB / ID: 6wl8
TitleCryo-EM of Form 2 peptide filament
ComponentsForm 2 peptide
KeywordsPROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang, F. / Gnewou, O.M. / Xu, C. / Su, Z. / 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 2 peptide filament
Authors: Wang, F. / Gnewou, O.M. / Xu, C. / Su, Z. / Egelman, E.H. / Conticello, V.P.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release

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Structure visualization

Movie
  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Form 2 peptide
0: Form 2 peptide
B: Form 2 peptide
2: Form 2 peptide
C: Form 2 peptide
3: Form 2 peptide
D: Form 2 peptide
4: Form 2 peptide
E: Form 2 peptide
5: Form 2 peptide
F: Form 2 peptide
6: Form 2 peptide
G: Form 2 peptide
7: Form 2 peptide
H: Form 2 peptide
8: Form 2 peptide
I: Form 2 peptide
9: Form 2 peptide
J: Form 2 peptide
AA: Form 2 peptide
K: Form 2 peptide
BA: Form 2 peptide
L: Form 2 peptide
CA: Form 2 peptide
M: Form 2 peptide
DA: Form 2 peptide
N: Form 2 peptide
EA: Form 2 peptide
O: Form 2 peptide
FA: Form 2 peptide
P: Form 2 peptide
GA: Form 2 peptide
Q: Form 2 peptide
HA: Form 2 peptide
R: Form 2 peptide
IA: Form 2 peptide
S: Form 2 peptide
JA: Form 2 peptide
T: Form 2 peptide
KA: Form 2 peptide
U: Form 2 peptide
LA: Form 2 peptide
V: Form 2 peptide
MA: Form 2 peptide
W: Form 2 peptide
NA: Form 2 peptide
X: Form 2 peptide
OA: Form 2 peptide
Y: Form 2 peptide
PA: Form 2 peptide
Z: Form 2 peptide
QA: Form 2 peptide
a: Form 2 peptide
RA: Form 2 peptide
b: Form 2 peptide
SA: Form 2 peptide
c: Form 2 peptide
TA: Form 2 peptide
d: Form 2 peptide
UA: Form 2 peptide
e: Form 2 peptide
VA: Form 2 peptide
f: Form 2 peptide
WA: Form 2 peptide
g: Form 2 peptide
XA: Form 2 peptide
h: Form 2 peptide
YA: Form 2 peptide
i: Form 2 peptide
ZA: Form 2 peptide
j: Form 2 peptide
aA: Form 2 peptide
k: Form 2 peptide
bA: Form 2 peptide
l: Form 2 peptide
cA: Form 2 peptide
m: Form 2 peptide
dA: Form 2 peptide
n: Form 2 peptide
eA: Form 2 peptide
o: Form 2 peptide
fA: Form 2 peptide
p: Form 2 peptide
gA: Form 2 peptide
q: Form 2 peptide
hA: Form 2 peptide
r: Form 2 peptide
iA: Form 2 peptide
s: Form 2 peptide
jA: Form 2 peptide
t: Form 2 peptide
kA: Form 2 peptide
u: Form 2 peptide
lA: Form 2 peptide
v: Form 2 peptide
mA: Form 2 peptide
w: Form 2 peptide
nA: Form 2 peptide
x: Form 2 peptide
oA: Form 2 peptide
y: Form 2 peptide
pA: Form 2 peptide
z: Form 2 peptide
qA: Form 2 peptide
1: Form 2 peptide
rA: Form 2 peptide


Theoretical massNumber of molelcules
Total (without water)338,961106
Polymers338,961106
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area185340 Å2
ΔGint-1851 kcal/mol
Surface area134320 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 106 / Rise per n subunits: 1.93 Å / Rotation per n subunits: 124.36 °)

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Components

#1: Protein/peptide ...
Form 2 peptide


Mass: 3197.741 Da / Num. of mol.: 106 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: self-assembly Form 2 peptide filament / 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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 124.36 ° / Axial rise/subunit: 1.93 Å / Axial symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: OTHER / Num. of particles: 408751 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL

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