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- PDB-3j89: Structural Plasticity of Helical Nanotubes Based on Coiled-Coil A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3j89 | ||||||
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Title | Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies | ||||||
![]() | synthetic peptide | ||||||
![]() | SYNTHETIC PEPTIDE / coiled-coil / nanotube / helical filament | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Egelman, E.H. / Xu, C. / DiMaio, F. / Magnotti, E. / Modlin, C. / Yu, X. / Wright, E. / Baker, D. / Conticello, V.P. | ||||||
![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 202.6 KB | Display | ![]() |
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PDB format | ![]() | 174 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6123MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Helical 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 °) |
Details | This 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 | Mass: 3309.797 Da / Num. of mol.: 19 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Helical nanotube formed from a 29-residue peptide / Type: COMPLEX |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS / Date: Aug 1, 2013 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4400 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 260 |
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Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: micrographs multiplied by CTF | ||||||||||||
Helical symmerty | Angular rotation/subunit: 87.1 ° / Axial rise/subunit: 2.2 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Method: 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 step | Cycle: LAST
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