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- EMDB-21817: Cryo-EM of Form 2 peptide filament -

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Basic information

Entry
Database: EMDB / ID: EMD-21817
TitleCryo-EM of Form 2 peptide filament
Map dataCryo-EM of Form 2 peptide filament
Sample
  • Complex: self-assembly Form 2 peptide filament
    • Protein or peptide: Form 2 peptide
Keywordsfilament / self-assembly peptide filament / Cryo-EM / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang F / Gnewou OM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.
Authors: Fengbin Wang / Ordy Gnewou / Charles Modlin / Leticia C Beltran / Chunfu Xu / Zhangli Su / Puneet Juneja / Gevorg Grigoryan / Edward H Egelman / Vincent P Conticello /
Abstract: The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of ...The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
History
DepositionApr 18, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0103
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0103
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wl8
  • Surface level: 0.0103
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wl8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21817.png

Downloads & links

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Map

FileDownload / File: emd_21817.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of Form 2 peptide filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0103 / Movie #1: 0.0103
Minimum - Maximum-0.013599785 - 0.045147005
Average (Standard dev.)0.00046599677 (±0.0030081703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0140.0450.000

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Supplemental data

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Sample components

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Entire : self-assembly Form 2 peptide filament

EntireName: self-assembly Form 2 peptide filament
Components
  • Complex: self-assembly Form 2 peptide filament
    • Protein or peptide: Form 2 peptide

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Supramolecule #1: self-assembly Form 2 peptide filament

SupramoleculeName: self-assembly Form 2 peptide filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: synthetic peptide
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Form 2 peptide

MacromoleculeName: Form 2 peptide / type: protein_or_peptide / ID: 1 / Number of copies: 106 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.197741 KDa
SequenceString:
QAKILEADAE ILKAYAKILE AHAEILKAQ

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 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: 1.93 Å
Applied symmetry - Helical parameters - Δ&Phi: 124.36 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Details: Model:Map FSC 0.38 cut off and d99 / Number images used: 408751
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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