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- PDB-6x5i: Cryo-EM of peptide-like filament of 1-KMe3 -

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Basic information

Entry
Database: PDB / ID: 6x5i
TitleCryo-EM of peptide-like filament of 1-KMe3
Components1-KMe3 peptide-like fibril
KeywordsPROTEIN FIBRIL / peptide-like fibril / helical symmetry
Function / homologypolypeptide(D)
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang, F. / Feng, Z. / Xu, B. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Cell Rep Phys Sci / Year: 2020
Title: Artificial Intracellular Filaments.
Authors: Zhaoqianqi Feng / Huaimin Wang / Fengbin Wang / Younghoon Oh / Cristina Berciu / Qiang Cui / Edward H Egelman / Bing Xu /
Abstract: Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the ...Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments.
History
DepositionMay 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 15, 2020Group: Database references / Non-polymer description / Category: chem_comp / citation
Item: _chem_comp.formula / _citation.journal_abbrev ..._chem_comp.formula / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22051
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Assembly

Deposited unit
B: 1-KMe3 peptide-like fibril
D: 1-KMe3 peptide-like fibril
E: 1-KMe3 peptide-like fibril
F: 1-KMe3 peptide-like fibril
G: 1-KMe3 peptide-like fibril
H: 1-KMe3 peptide-like fibril
I: 1-KMe3 peptide-like fibril
J: 1-KMe3 peptide-like fibril
K: 1-KMe3 peptide-like fibril
L: 1-KMe3 peptide-like fibril
M: 1-KMe3 peptide-like fibril
N: 1-KMe3 peptide-like fibril
O: 1-KMe3 peptide-like fibril
P: 1-KMe3 peptide-like fibril
Q: 1-KMe3 peptide-like fibril
R: 1-KMe3 peptide-like fibril
S: 1-KMe3 peptide-like fibril
T: 1-KMe3 peptide-like fibril
U: 1-KMe3 peptide-like fibril
V: 1-KMe3 peptide-like fibril
W: 1-KMe3 peptide-like fibril
X: 1-KMe3 peptide-like fibril
Y: 1-KMe3 peptide-like fibril
Z: 1-KMe3 peptide-like fibril
a: 1-KMe3 peptide-like fibril
b: 1-KMe3 peptide-like fibril
c: 1-KMe3 peptide-like fibril
d: 1-KMe3 peptide-like fibril
e: 1-KMe3 peptide-like fibril
f: 1-KMe3 peptide-like fibril
g: 1-KMe3 peptide-like fibril
h: 1-KMe3 peptide-like fibril
i: 1-KMe3 peptide-like fibril
j: 1-KMe3 peptide-like fibril
k: 1-KMe3 peptide-like fibril
l: 1-KMe3 peptide-like fibril
m: 1-KMe3 peptide-like fibril
n: 1-KMe3 peptide-like fibril
o: 1-KMe3 peptide-like fibril
p: 1-KMe3 peptide-like fibril
q: 1-KMe3 peptide-like fibril
r: 1-KMe3 peptide-like fibril
s: 1-KMe3 peptide-like fibril
t: 1-KMe3 peptide-like fibril
u: 1-KMe3 peptide-like fibril
v: 1-KMe3 peptide-like fibril
w: 1-KMe3 peptide-like fibril
x: 1-KMe3 peptide-like fibril
y: 1-KMe3 peptide-like fibril
z: 1-KMe3 peptide-like fibril
0: 1-KMe3 peptide-like fibril
AA: 1-KMe3 peptide-like fibril
BA: 1-KMe3 peptide-like fibril
CA: 1-KMe3 peptide-like fibril
DA: 1-KMe3 peptide-like fibril
EA: 1-KMe3 peptide-like fibril
FA: 1-KMe3 peptide-like fibril
GA: 1-KMe3 peptide-like fibril
HA: 1-KMe3 peptide-like fibril
IA: 1-KMe3 peptide-like fibril
JA: 1-KMe3 peptide-like fibril
KA: 1-KMe3 peptide-like fibril
LA: 1-KMe3 peptide-like fibril
MA: 1-KMe3 peptide-like fibril
NA: 1-KMe3 peptide-like fibril
OA: 1-KMe3 peptide-like fibril
PA: 1-KMe3 peptide-like fibril
QA: 1-KMe3 peptide-like fibril
RA: 1-KMe3 peptide-like fibril
SA: 1-KMe3 peptide-like fibril


Theoretical massNumber of molelcules
Total (without water)61,66870
Polymers61,66870
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: 7 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 4.9 Å / Rotation per n subunits: 2.3 °)

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Components

#1: Polypeptide(D) ...
1-KMe3 peptide-like fibril


Mass: 880.965 Da / Num. of mol.: 70 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: 1-KMe3 peptide-like fibril / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
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: 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 K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 2.3 ° / Axial rise/subunit: 4.9 Å / Axial symmetry: C7
3D reconstructionResolution: 4.3 Å / Resolution method: OTHER / Num. of particles: 108886 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL

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