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- PDB-7lqg: Cryo-EM of the KFE8 thinner nanotube (class 1, C2) -

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Basic information

Entry
Database: PDB / ID: 7lqg
TitleCryo-EM of the KFE8 thinner nanotube (class 1, C2)
ComponentsKFE8 peptide
KeywordsPROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM / peptide fibril / nanotube
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 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: Matter / Year: 2021
Title: Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide.
Authors: Fengbin Wang / Ordy Gnewou / Shengyuan Wang / Tomasz Osinski / Xiaobing Zuo / Edward H Egelman / Vincent P Conticello /
Abstract: The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical ...The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.
History
DepositionFeb 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2

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Structure visualization

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Assembly

Deposited unit
A: KFE8 peptide
J: KFE8 peptide
K: KFE8 peptide
L: KFE8 peptide
M: KFE8 peptide
N: KFE8 peptide
O: KFE8 peptide
P: KFE8 peptide
B: KFE8 peptide
Q: KFE8 peptide
R: KFE8 peptide
S: KFE8 peptide
T: KFE8 peptide
U: KFE8 peptide
V: KFE8 peptide
W: KFE8 peptide
C: KFE8 peptide
X: KFE8 peptide
Y: KFE8 peptide
Z: KFE8 peptide
j: KFE8 peptide
k: KFE8 peptide
l: KFE8 peptide
m: KFE8 peptide
D: KFE8 peptide
n: KFE8 peptide
o: KFE8 peptide
p: KFE8 peptide
q: KFE8 peptide
r: KFE8 peptide
s: KFE8 peptide
t: KFE8 peptide
E: KFE8 peptide
u: KFE8 peptide
v: KFE8 peptide
w: KFE8 peptide
x: KFE8 peptide
y: KFE8 peptide
z: KFE8 peptide
0: KFE8 peptide
F: KFE8 peptide
1: KFE8 peptide
2: KFE8 peptide
3: KFE8 peptide
4: KFE8 peptide
5: KFE8 peptide
6: KFE8 peptide
7: KFE8 peptide
G: KFE8 peptide
8: KFE8 peptide
9: KFE8 peptide
AA: KFE8 peptide
BA: KFE8 peptide
CA: KFE8 peptide
DA: KFE8 peptide
EA: KFE8 peptide
H: KFE8 peptide
FA: KFE8 peptide
GA: KFE8 peptide
HA: KFE8 peptide
IA: KFE8 peptide
JA: KFE8 peptide
KA: KFE8 peptide
LA: KFE8 peptide
I: KFE8 peptide
MA: KFE8 peptide
NA: KFE8 peptide
OA: KFE8 peptide
PA: KFE8 peptide
QA: KFE8 peptide
RA: KFE8 peptide
SA: KFE8 peptide
a: KFE8 peptide
TA: KFE8 peptide
UA: KFE8 peptide
VA: KFE8 peptide
WA: KFE8 peptide
XA: KFE8 peptide
YA: KFE8 peptide
ZA: KFE8 peptide
b: KFE8 peptide
aA: KFE8 peptide
bA: KFE8 peptide
cA: KFE8 peptide
dA: KFE8 peptide
eA: KFE8 peptide
fA: KFE8 peptide
gA: KFE8 peptide
c: KFE8 peptide
hA: KFE8 peptide
iA: KFE8 peptide
jA: KFE8 peptide
kA: KFE8 peptide
lA: KFE8 peptide
mA: KFE8 peptide
nA: KFE8 peptide
d: KFE8 peptide
oA: KFE8 peptide
pA: KFE8 peptide
qA: KFE8 peptide
rA: KFE8 peptide
sA: KFE8 peptide
tA: KFE8 peptide
uA: KFE8 peptide
e: KFE8 peptide
vA: KFE8 peptide
wA: KFE8 peptide
xA: KFE8 peptide
yA: KFE8 peptide
zA: KFE8 peptide
0A: KFE8 peptide
1A: KFE8 peptide
f: KFE8 peptide
2A: KFE8 peptide
3A: KFE8 peptide
4A: KFE8 peptide
5A: KFE8 peptide
6A: KFE8 peptide
7A: KFE8 peptide
8A: KFE8 peptide
g: KFE8 peptide
9A: KFE8 peptide
AB: KFE8 peptide
BB: KFE8 peptide
CB: KFE8 peptide
DB: KFE8 peptide
EB: KFE8 peptide
FB: KFE8 peptide
h: KFE8 peptide
GB: KFE8 peptide
HB: KFE8 peptide
IB: KFE8 peptide
JB: KFE8 peptide
KB: KFE8 peptide
LB: KFE8 peptide
MB: KFE8 peptide
i: KFE8 peptide
NB: KFE8 peptide
OB: KFE8 peptide
PB: KFE8 peptide
QB: KFE8 peptide
RB: KFE8 peptide
SB: KFE8 peptide
TB: KFE8 peptide


Theoretical massNumber of molelcules
Total (without water)167,666144
Polymers167,666144
Non-polymers00
Water00
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
SymmetryHelical symmetry: (Circular symmetry: 2 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 144 / Rise per n subunits: 7.93 Å / Rotation per n subunits: -15.8 °)

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Components

#1: Protein/peptide ...
KFE8 peptide


Mass: 1164.350 Da / Num. of mol.: 144 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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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 KFE8 nanotubes / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 4
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 FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -15.8 ° / Axial rise/subunit: 7.93 Å / Axial symmetry: C2
3D reconstructionResolution: 3.4 Å / Resolution method: OTHER / Num. of particles: 15486 / Details: Model:Map FSC 0.38 cut off / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00812384
ELECTRON MICROSCOPYf_angle_d0.86415840
ELECTRON MICROSCOPYf_dihedral_angle_d22.5646048
ELECTRON MICROSCOPYf_chiral_restr0.0531152
ELECTRON MICROSCOPYf_plane_restr0.0022016

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