7OE2

Model of closed pentamer of the Haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment.

Ross, J.McIver, Z.Lambert, T.Piergentili, C.Bird, J.E.Gallagher, K.J.Cruickshank, F.L.James, P.Zarazua-Arvizu, E.Horsfall, L.E.Waldron, K.J.Wilson, M.D.Mackay, C.L.Basle, A.Clarke, D.J.Marles-Wright, J.

(2022) Sci Adv 8: eabj4461-eabj4461

  • DOI: https://doi.org/10.1126/sciadv.abj4461
  • Primary Citation of Related Structures:  
    7ODW, 7OE2, 7OEU

  • PubMed Abstract: 

    Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.


  • Organizational Affiliation

    EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Linocin_M18 bacteriocin protein
A, B, C, D, E
266Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_3837
UniProt
Find proteins for D0LZ74 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LZ74 
Go to UniProtKB:  D0LZ74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LZ74
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Haliangium ochraceum Encapsulated ferritin localisation sequenceF [auth 1],
G [auth 2],
H [auth 3],
I [auth 4],
J [auth 5]
131Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_3836
UniProt
Find proteins for D0LZ73 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LZ73 
Go to UniProtKB:  D0LZ73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LZ73
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N005570/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release