3DKT | pdb_00003dkt

Crystal structure of Thermotoga maritima encapsulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.239 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 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: https://doi.org/10.1038/nsmb.1473
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 313.34 kDa 
  • Atom Count: 22,070 
  • Modeled Residue Count: 2,720 
  • Deposited Residue Count: 2,730 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maritimacin
A, B, C, D, E
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZP2
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
K, L, M, N, O
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
Entity Groups
UniProt GroupQ9WZP3
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.239 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
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

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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
  • Version 1.5: 2024-03-20
    Changes: Data collection, Database references, Refinement description