3J89 | pdb_00003j89

Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies

• PDB DOI: https://doi.org/10.2210/pdb3J89/pdb
• EM Map EMD-6123: EMDB EMDataResource

• Classification: SYNTHETIC PEPTIDE
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2014-10-07 Released: 2015-02-11 
• Deposition Author(s): Egelman, E.H., Xu, C., DiMaio, F., Magnotti, E., Modlin, C., Yu, X., Wright, E., Baker, D., Conticello, V.P.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Structural plasticity of helical nanotubes based on coiled-coil assemblies.

Egelman, E.H., Xu, C., DiMaio, F., Magnotti, E., Modlin, C., Yu, X., Wright, E., Baker, D., Conticello, V.P.

(2015) Structure 23: 280-289

• PubMed: 25620001 
• DOI: https://doi.org/10.1016/j.str.2014.12.008
• Primary Citation Related Structures: 
  3J89


• PubMed 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 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.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address: [e-mail].
Department of Chemistry, Emory University, Atlanta, GA 30322, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
Department of Chemistry, Emory University, Atlanta, GA 30322, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 19-mer - A19 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.89 kDa 
• Atom Count: 4,427 
• Modeled Residue Count: 551 
• Deposited Residue Count: 551 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
synthetic peptide	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S	29	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Egelman, E.H., Xu, C., DiMaio, F., Magnotti, E., Modlin, C., Yu, X., Wright, E., Baker, D., Conticello, V.P.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references