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- PDB-6wkx: Cryo-EM of Form 1 related peptide filament, 15-10-3 -

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Basic information

Entry
Database: PDB / ID: 6wkx
TitleCryo-EM of Form 1 related peptide filament, 15-10-3
Componentspeptide 15-10-3
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, 15-10-3
Authors: Wang, F. / Gnewou, O.M. / Egelman, E.H. / Conticello, V.P.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: peptide 15-10-3
V: peptide 15-10-3
W: peptide 15-10-3
X: peptide 15-10-3
Y: peptide 15-10-3
B: peptide 15-10-3
Z: peptide 15-10-3
a: peptide 15-10-3
b: peptide 15-10-3
c: peptide 15-10-3
C: peptide 15-10-3
d: peptide 15-10-3
e: peptide 15-10-3
f: peptide 15-10-3
g: peptide 15-10-3
D: peptide 15-10-3
h: peptide 15-10-3
i: peptide 15-10-3
j: peptide 15-10-3
k: peptide 15-10-3
E: peptide 15-10-3
l: peptide 15-10-3
m: peptide 15-10-3
n: peptide 15-10-3
o: peptide 15-10-3
F: peptide 15-10-3
p: peptide 15-10-3
q: peptide 15-10-3
r: peptide 15-10-3
s: peptide 15-10-3
G: peptide 15-10-3
t: peptide 15-10-3
u: peptide 15-10-3
v: peptide 15-10-3
w: peptide 15-10-3
H: peptide 15-10-3
x: peptide 15-10-3
y: peptide 15-10-3
z: peptide 15-10-3
0: peptide 15-10-3
I: peptide 15-10-3
1: peptide 15-10-3
2: peptide 15-10-3
3: peptide 15-10-3
4: peptide 15-10-3
J: peptide 15-10-3
5: peptide 15-10-3
6: peptide 15-10-3
7: peptide 15-10-3
8: peptide 15-10-3
K: peptide 15-10-3
9: peptide 15-10-3
AA: peptide 15-10-3
BA: peptide 15-10-3
CA: peptide 15-10-3
L: peptide 15-10-3
DA: peptide 15-10-3
EA: peptide 15-10-3
FA: peptide 15-10-3
GA: peptide 15-10-3
M: peptide 15-10-3
HA: peptide 15-10-3
IA: peptide 15-10-3
JA: peptide 15-10-3
KA: peptide 15-10-3
N: peptide 15-10-3
LA: peptide 15-10-3
MA: peptide 15-10-3
NA: peptide 15-10-3
OA: peptide 15-10-3
O: peptide 15-10-3
PA: peptide 15-10-3
QA: peptide 15-10-3
RA: peptide 15-10-3
SA: peptide 15-10-3
P: peptide 15-10-3
TA: peptide 15-10-3
UA: peptide 15-10-3
VA: peptide 15-10-3
WA: peptide 15-10-3
Q: peptide 15-10-3
XA: peptide 15-10-3
YA: peptide 15-10-3
ZA: peptide 15-10-3
aA: peptide 15-10-3
R: peptide 15-10-3
bA: peptide 15-10-3
cA: peptide 15-10-3
dA: peptide 15-10-3
eA: peptide 15-10-3
S: peptide 15-10-3
fA: peptide 15-10-3
gA: peptide 15-10-3
hA: peptide 15-10-3
iA: peptide 15-10-3
T: peptide 15-10-3
jA: peptide 15-10-3
kA: peptide 15-10-3
lA: peptide 15-10-3
mA: peptide 15-10-3
U: peptide 15-10-3
nA: peptide 15-10-3
oA: peptide 15-10-3
pA: peptide 15-10-3
qA: peptide 15-10-3


Theoretical massNumber of molelcules
Total (without water)183,435105
Polymers183,435105
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 area126730 Å2
ΔGint-349 kcal/mol
Surface area51370 Å2
SymmetryHelical symmetry: (Circular symmetry: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 105 / Rise per n subunits: 9.23 Å / Rotation per n subunits: 9.31 °)

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Components

#1: Protein/peptide ...
peptide 15-10-3


Mass: 1747.004 Da / Num. of mol.: 105 / 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 peptide filament, 15-10-3 / 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

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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 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 9.31 ° / Axial rise/subunit: 9.23 Å / Axial symmetry: C5
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 14700 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612915
ELECTRON MICROSCOPYf_angle_d0.52817325
ELECTRON MICROSCOPYf_dihedral_angle_d20.6828190
ELECTRON MICROSCOPYf_chiral_restr0.0381995
ELECTRON MICROSCOPYf_plane_restr0.0022310

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