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- EMDB-6123: Helical nanotube formed from a 29-residue peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-6123
TitleHelical nanotube formed from a 29-residue peptide
Map datareconstruction of Form I polymer
Sample
  • Sample: synthetic peptide
  • Protein or peptide: synthetic peptide
KeywordsIHRSR / polymorphism / coiled-coils
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsEgelman EH / Xu C / DiMaio F / Magnotti E / Modlin C / Yu X / Wright E / Baker D / Conticello VP
CitationJournal: Structure / Year: 2015
Title: Structural plasticity of helical nanotubes based on coiled-coil assemblies.
Authors: E H Egelman / C Xu / F DiMaio / E Magnotti / C Modlin / X Yu / E Wright / D Baker / V P Conticello /
Abstract: Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through ...Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure, in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.
History
DepositionOct 6, 2014-
Header (metadata) releaseOct 15, 2014-
Map releaseFeb 11, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j89
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6123.gif

Downloads & links

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Map

FileDownload / File: emd_6123.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of Form I polymer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 100 pix.
= 102. Å		1.02 Å/pix.
x 100 pix.
= 102. Å		1.02 Å/pix.
x 100 pix.
= 102. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-1.25968301 - 3.77647614
Average (Standard dev.)0.04744104 (±0.27348593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 102.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z102.000102.000102.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-1.2603.7760.047

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Supplemental data

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Sample components

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Entire : synthetic peptide

EntireName: synthetic peptide (others)
Components
  • Sample: synthetic peptide
  • Protein or peptide: synthetic peptide

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Supramolecule #1000: synthetic peptide

SupramoleculeName: synthetic peptide / type: sample / ID: 1000 / Oligomeric state: polymer / Number unique components: 1

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Macromolecule #1: synthetic peptide

MacromoleculeName: synthetic peptide / type: protein_or_peptide / ID: 1 / Details: QARILEADAEILRAYARILEAHAEILRAQ / Recombinant expression: No / Database: NCBI
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateAug 1, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 260 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.4 µm / Nominal defocus min: 1.4 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsIHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 87.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: Spider
CTF correctionDetails: micrographs multiplied by CTF

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