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- PDB-6wl9: Cryo-EM of Form 2 like peptide filament, Form2a -

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Basic information

Entry
Database: PDB / ID: 6wl9
TitleCryo-EM of Form 2 like peptide filament, Form2a
Componentspeptide Form2a
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. / Beltran, L.C. / 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 2 like peptide filament, Form2a
Authors: Wang, F. / Beltran, L.C. / Gnewou, O.M. / 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

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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: peptide Form2a
0: peptide Form2a
B: peptide Form2a
1: peptide Form2a
C: peptide Form2a
2: peptide Form2a
D: peptide Form2a
3: peptide Form2a
E: peptide Form2a
4: peptide Form2a
F: peptide Form2a
5: peptide Form2a
G: peptide Form2a
6: peptide Form2a
H: peptide Form2a
7: peptide Form2a
I: peptide Form2a
8: peptide Form2a
J: peptide Form2a
9: peptide Form2a
K: peptide Form2a
AA: peptide Form2a
L: peptide Form2a
BA: peptide Form2a
M: peptide Form2a
CA: peptide Form2a
N: peptide Form2a
DA: peptide Form2a
O: peptide Form2a
EA: peptide Form2a
P: peptide Form2a
FA: peptide Form2a
Q: peptide Form2a
GA: peptide Form2a
R: peptide Form2a
HA: peptide Form2a
S: peptide Form2a
IA: peptide Form2a
T: peptide Form2a
JA: peptide Form2a
U: peptide Form2a
KA: peptide Form2a
V: peptide Form2a
LA: peptide Form2a
W: peptide Form2a
MA: peptide Form2a
X: peptide Form2a
NA: peptide Form2a
Y: peptide Form2a
OA: peptide Form2a
Z: peptide Form2a
PA: peptide Form2a
a: peptide Form2a
QA: peptide Form2a
b: peptide Form2a
RA: peptide Form2a
c: peptide Form2a
SA: peptide Form2a
d: peptide Form2a
TA: peptide Form2a
e: peptide Form2a
UA: peptide Form2a
f: peptide Form2a
VA: peptide Form2a
g: peptide Form2a
WA: peptide Form2a
h: peptide Form2a
XA: peptide Form2a
i: peptide Form2a
YA: peptide Form2a
j: peptide Form2a
ZA: peptide Form2a
k: peptide Form2a
aA: peptide Form2a
l: peptide Form2a
bA: peptide Form2a
m: peptide Form2a
cA: peptide Form2a
n: peptide Form2a
dA: peptide Form2a
o: peptide Form2a
eA: peptide Form2a
p: peptide Form2a
fA: peptide Form2a
q: peptide Form2a
gA: peptide Form2a
r: peptide Form2a
hA: peptide Form2a
s: peptide Form2a
iA: peptide Form2a
t: peptide Form2a
jA: peptide Form2a
u: peptide Form2a
kA: peptide Form2a
v: peptide Form2a
lA: peptide Form2a
w: peptide Form2a
mA: peptide Form2a
x: peptide Form2a
nA: peptide Form2a
y: peptide Form2a
oA: peptide Form2a
z: peptide Form2a
pA: peptide Form2a


Theoretical massNumber of molelcules
Total (without water)332,565104
Polymers332,565104
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 area165900 Å2
ΔGint-1790 kcal/mol
Surface area133220 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 104 / Rise per n subunits: 1.92 Å / Rotation per n subunits: 124.37 °)

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Components

#1: Protein/peptide ...
peptide Form2a


Mass: 3197.741 Da / Num. of mol.: 104 / 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, Form2a / 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: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 124.37 ° / Axial rise/subunit: 1.92 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 288990 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00623504
ELECTRON MICROSCOPYf_angle_d0.51231512
ELECTRON MICROSCOPYf_dihedral_angle_d2.7114976
ELECTRON MICROSCOPYf_chiral_restr0.0413848
ELECTRON MICROSCOPYf_plane_restr0.0023952

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