3DKT

Crystal structure of Thermotoga maritima encapsulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.104 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maritimacin
A, B, C, D, E, F, G, H, I, J
265Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
EC: 3.4.-.-
Find proteins for Q9WZP2 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WZP2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
K, L, M, N, O, P, Q, R, S, T
8Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Find proteins for Q9WZP3 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WZP3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.104 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • Space Group: F 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 669.040α = 90.00
b = 669.040β = 90.00
c = 669.040γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement
XDSdata scaling
AVE/DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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