4W8X

Crystal Structure of Cmr1 from Pyrococcus furiosus bound to a nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4.

Benda, C.Ebert, J.Scheltema, R.A.Schiller, H.B.Baumgartner, M.Bonneau, F.Mann, M.Conti, E.

(2014) Mol.Cell 56: 43-54

  • DOI: 10.1016/j.molcel.2014.09.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system. We investigated the molecular architecture of the P. furiosus Cmr complex using an integrative structural biology approac ...

    The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system. We investigated the molecular architecture of the P. furiosus Cmr complex using an integrative structural biology approach. We determined crystal structures of P. furiosus Cmr1, Cmr2, Cmr4, and Cmr6 and combined them with known structural information to interpret the cryo-EM map of the complex. To support structure determination, we obtained residue-specific interaction data using protein crosslinking and mass spectrometry. The resulting pseudoatomic model reveals how the superhelical backbone of the complex is defined by the polymerizing principles of Cmr4 and Cmr5 and how it is capped at the extremities by proteins of similar folds. The inner surface of the superhelix exposes conserved residues of Cmr4 that we show are required for target-cleavage activity. The structural and biochemical data thus identify Cmr4 as the conserved endoribonuclease of the Cmr complex.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. Electronic address: conti@biochem.mpg.de.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cmr subunit Cmr1-1
A
344Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: cmr1-1
Find proteins for Q8U1S5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U1S5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
3GP
Query on 3GP

Download SDF File 
Download CCD File 
A
GUANOSINE-3'-MONOPHOSPHATE
C10 H14 N5 O8 P
ZDPUTNZENXVHJC-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.057α = 90.00
b = 101.057β = 90.00
c = 107.947γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyFOR1680
ERCGermany294371

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release