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- PDB-3j89: Structural Plasticity of Helical Nanotubes Based on Coiled-Coil A... -

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Entry
Database: PDB / ID: 3j89
TitleStructural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies
Componentssynthetic peptide
KeywordsSYNTHETIC PEPTIDE / coiled-coil / nanotube / helical filament
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsEgelman, E.H. / Xu, C. / DiMaio, F. / Magnotti, E. / Modlin, C. / Yu, X. / Wright, E. / Baker, D. / Conticello, V.P.
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 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: synthetic peptide
B: synthetic peptide
C: synthetic peptide
D: synthetic peptide
E: synthetic peptide
F: synthetic peptide
G: synthetic peptide
H: synthetic peptide
I: synthetic peptide
J: synthetic peptide
K: synthetic peptide
L: synthetic peptide
M: synthetic peptide
N: synthetic peptide
O: synthetic peptide
P: synthetic peptide
Q: synthetic peptide
R: synthetic peptide
S: synthetic peptide


Theoretical massNumber of molelcules
Total (without water)62,88619
Polymers62,88619
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 19 / Rise per n subunits: 2.2 Å / Rotation per n subunits: -87.1 °)
DetailsThis peptide forms a helical nanotube of indeterminate length. The designation "nonadecameric" in REMARK 350 is an artifact of the PDB format and can be disregarded.

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Components

#1: Protein/peptide
synthetic peptide


Mass: 3309.797 Da / Num. of mol.: 19 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical nanotube formed from a 29-residue peptide / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4400 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 10 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 260

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: micrographs multiplied by CTF
Helical symmertyAngular rotation/subunit: 87.1 ° / Axial rise/subunit: 2.2 Å / Axial symmetry: C1
3D reconstructionMethod: IHRSR / Resolution: 3.6 Å / Resolution method: OTHER / Nominal pixel size: 1.02 Å / Actual pixel size: 1.02 Å
Details: Both FSC and comparison with atomic model used for resolution determination.
Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4427 0 0 0 4427

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