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- EMDB-22051: Cryo-EM of peptide-like filament of 1-KMe3 -

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Basic information

Entry
Database: EMDB / ID: EMD-22051
TitleCryo-EM of peptide-like filament of 1-KMe3
Map dataCryo-EM of peptide-like filaments of 1-KMe3
Sample
  • Complex: 1-KMe3 peptide-like fibril
    • Protein or peptide: 1-KMe3 peptide-like fibril
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang F / Feng Z / Xu B / Egelman EH
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateAug 26, 2020-
Current statusAug 26, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000696
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.000696
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x5i
  • Surface level: 0.0007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22051.png

Downloads & links

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Map

FileDownload / File: emd_22051.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of peptide-like filaments of 1-KMe3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 120 pix.
= 127.2 Å		1.06 Å/pix.
x 120 pix.
= 127.2 Å		1.06 Å/pix.
x 120 pix.
= 127.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000696 / Movie #1: 0.000696
Minimum - Maximum0.0000441710 - 0.0011079364
Average (Standard dev.)0.0003054947 (±0.00019088073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 127.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z127.200127.200127.200
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean0.0000.0010.000

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Supplemental data

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Sample components

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Entire : 1-KMe3 peptide-like fibril

EntireName: 1-KMe3 peptide-like fibril
Components
  • Complex: 1-KMe3 peptide-like fibril
    • Protein or peptide: 1-KMe3 peptide-like fibril

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Supramolecule #1: 1-KMe3 peptide-like fibril

SupramoleculeName: 1-KMe3 peptide-like fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1-KMe3 peptide-like fibril

MacromoleculeName: 1-KMe3 peptide-like fibril / type: protein_or_peptide / ID: 1 / Number of copies: 70 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 880.965 Da
SequenceString:
(UQ4)(DPN)(DPN)(DTY)(M3L)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 2.3 °
Applied symmetry - Helical parameters - Axial symmetry: C7 (7 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Number images used: 108886
Startup modelType of model: OTHER
Details: averaged cylinder using all segments, with random azimuthal angles
Final angle assignmentType: NOT APPLICABLE

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