6TUG

Enterococcus italicus Csm6 bound to cyclic hexa-2'-fluoro-hexa-dAMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6.

Garcia-Doval, C.Schwede, F.Berk, C.Rostol, J.T.Niewoehner, O.Tejero, O.Hall, J.Marraffini, L.A.Jinek, M.

(2020) Nat Commun 11: 1596-1596

  • DOI: https://doi.org/10.1038/s41467-020-15334-5
  • Primary Citation of Related Structures:  
    6TUG

  • PubMed Abstract: 

    Bacterial and archaeal CRISPR-Cas systems provide RNA-guided immunity against genetic invaders such as bacteriophages and plasmids. Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic-oligoadenylate second messengers that activate downstream effectors, including Csm6 ribonucleases, via their CARF domains. Here, we show that Enteroccocus italicus Csm6 (EiCsm6) degrades its cognate cyclic hexa-AMP (cA6) activator, and report the crystal structure of EiCsm6 bound to a cA6 mimic. Our structural, biochemical, and in vivo functional assays reveal how cA6 recognition by the CARF domain activates the Csm6 HEPN domains for collateral RNA degradation, and how CARF domain-mediated cA6 cleavage provides an intrinsic off-switch to limit Csm6 activity in the absence of ring nucleases. These mechanisms facilitate rapid invader clearance and ensure termination of CRISPR interference to limit self-toxicity.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system endoribonuclease Csm6
A, B, C, D, E
A, B, C, D, E, F, G, H
433Enterococcus italicus DSM 15952Mutation(s): 0 
Gene Names: csm6HMPREF9088_1942
EC: 3.1
UniProt
Find proteins for E6LHV2 (Enterococcus italicus (strain DSM 15952 / CCUG 50447 / LMG 22039 / TP 1.5))
Explore E6LHV2 
Go to UniProtKB:  E6LHV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6LHV2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AF2 (Subject of Investigation/LOI)
Query on AF2

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
EA [auth G]
FA [auth G]
AA [auth F],
BA [auth F],
DA [auth G],
EA [auth G],
FA [auth G],
HA [auth H],
I [auth A],
IA [auth H],
J [auth A],
JA [auth H],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
V [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth F]
2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate)
C10 H13 F N5 O6 P
WMEBOUQKZKATDW-QYYRPYCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth F],
GA [auth G],
O [auth B],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.604α = 90.033
b = 106.686β = 90.007
c = 116.793γ = 90.1
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing
AutoPROCdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-CoG-820152
Swiss National Science FoundationSwitzerland205321_169612
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP1GM128184

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references