6HQE

Cryo-EM of self-assembly peptide filament LRV_M3delta1

PDB DOI: https://doi.org/10.2210/pdb6HQE/pdb
EM Map EMD-0252: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Azotobacter vinelandii
Mutation(s): No

Deposited: 2018-09-24 Released: 2019-06-26
Deposition Author(s): Osinski, T., Wang, F., Hughes, S.A., Kreutzberger, M.A.B., Conticello, V.P., Egelman, E.H.
Funding Organization(s): National Science Foundation (United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs.

Hughes, S.A., Wang, F., Wang, S., Kreutzberger, M.A.B., Osinski, T., Orlova, A., Wall, J.S., Zuo, X., Egelman, E.H., Conticello, V.P.

(2019) Proc Natl Acad Sci U S A 116: 14456-14464

PubMed: 31262809 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.1903910116
Primary Citation of Related Structures:
6HQE, 6MK1

PubMed 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 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.

Organizational Affiliation

Department of Chemistry, Emory University, Atlanta, GA 30322.

Macromolecule Content

Total Structure Weight: 134.16 kDa
Atom Count: 9,360
Modelled Residue Count: 1,196
Deposited Residue Count: 1,196
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide LRV_M3delta1	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	23	Azotobacter vinelandii	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence