7LIJ

Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pore structure controls stability and molecular flux in engineered protein cages.

Adamson, L.S.R.Tasneem, N.Andreas, M.P.Close, W.Jenner, E.N.Szyszka, T.N.Young, R.Cheah, L.C.Norman, A.MacDermott-Opeskin, H.I.O'Mara, M.L.Sainsbury, F.Giessen, T.W.Lau, Y.H.

(2022) Sci Adv 8: eabl7346-eabl7346

  • DOI: https://doi.org/10.1126/sciadv.abl7346
  • Primary Citation of Related Structures:  
    7LII, 7LIJ, 7LIK, 7LIL, 7LIM, 7LIS, 7LIT

  • PubMed Abstract: 

    Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the Thermotoga maritima encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux.


  • Organizational Affiliation

    School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maritimacin265Thermotoga maritima MSB8Mutation(s): 1 
Gene Names: TM_0785
EC: 3.4
UniProt
Find proteins for Q9WZP2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZP2 
Go to UniProtKB:  Q9WZP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZP2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download Ideal Coordinates CCD File 
B [auth A]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15.0
MODEL REFINEMENTPHENIX1.18.2-3874-000

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE190100624
Other privateAustraliaWRF2020
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133325

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection, Refinement description