3DKT

Crystal structure of Thermotoga maritima encapsulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of enzyme encapsulation into a bacterial nanocompartment

Sutter, M.Boehringer, D.Gutmann, S.Gunther, S.Prangishvili, D.Loessner, M.J.Stetter, K.O.Weber-Ban, E.Ban, N.

(2008) Nat Struct Mol Biol 15: 939-947

  • DOI: 10.1038/nsmb.1473
  • Primary Citation of Related Structures:  
    3DKT

  • PubMed Abstract: 
  • Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood ...

    Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood. Here we show, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-angstroms resolution reveals that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 angstroms. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response.


    Organizational Affiliation

    ETH Zurich, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, 8093 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maritimacin
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
265Thermotoga maritimaMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized protein
K, L, M, N, O, P, Q, R
K, L, M, N, O, P, Q, R, S, T
8Thermotoga maritimaMutation(s): 0 
UniProt
Find proteins for Q9WZP3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZP3 
Go to UniProtKB:  Q9WZP3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 669.04α = 90
b = 669.04β = 90
c = 669.04γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
AVE/DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Database references
  • Version 1.3: 2011-08-31
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2019-11-06
    Changes: Data collection