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- EMDB-0252: Cryo-EM of self-assembly peptide filament LRV_M3delta1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0252
TitleCryo-EM of self-assembly peptide filament LRV_M3delta1
Map data
Sample
  • Complex: self-assembly peptide filament
    • Protein or peptide: peptide LRV_M3delta1
Keywordsfilament / self-assembly peptide filament / Cryo-EM / PROTEIN FIBRIL
Biological speciesAzotobacter vinelandii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsOsinski T / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (United States)NSF-DMR-1533958 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs.
Authors: Spencer A Hughes / Fengbin Wang / Shengyuan Wang / Mark A B Kreutzberger / Tomasz Osinski / Albina Orlova / Joseph S Wall / Xiaobing Zuo / Edward H Egelman / Vincent P Conticello /
Abstract: Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 ...Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
History
DepositionSep 24, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseJun 26, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hqe
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hqe
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0252.png

Downloads & links

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Map

FileDownload / File: emd_0252.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 128 pix.
= 168.96 Å		1.32 Å/pix.
x 128 pix.
= 168.96 Å		1.32 Å/pix.
x 128 pix.
= 168.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002 / Movie #1: 0.002
Minimum - Maximum-0.0045427736 - 0.0063288664
Average (Standard dev.)0.00014172817 (±0.0006924727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 168.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z168.960168.960168.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0050.0060.000

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Supplemental data

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Sample components

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Entire : self-assembly peptide filament

EntireName: self-assembly peptide filament
Components
  • Complex: self-assembly peptide filament
    • Protein or peptide: peptide LRV_M3delta1

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Supramolecule #1: self-assembly peptide filament

SupramoleculeName: self-assembly peptide filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii (bacteria)

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Macromolecule #1: peptide LRV_M3delta1

MacromoleculeName: peptide LRV_M3delta1 / type: protein_or_peptide / ID: 1 / Number of copies: 52 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 2.579933 KDa
SequenceString:
PEALERLAAD PDREVRAAVA RRL

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 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: 1.15 Å
Applied symmetry - Helical parameters - Δ&Phi: -20.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: OTHER / Software - Name: SPIDER / Details: Model:Map FSC 0.38 cut off, d99 and d model / Number images used: 62616
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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