6SCE | pdb_00006sce

Structure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate

• PDB DOI: https://doi.org/10.2210/pdb6SCE/pdb
• NAKB: 6SCE

• Classification: DNA
• Organism(s): Thermus thermophilus HB8, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-24 Released: 2020-02-19 
• Deposition Author(s): McMahon, S.A., Zhu, W., Graham, S., White, M.F., Gloster, T.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.209 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate.

McMahon, S.A., Zhu, W., Graham, S., Rambo, R., White, M.F., Gloster, T.M.

(2020) Nat Commun 11: 500-500

• PubMed: 31980625 
• DOI: https://doi.org/10.1038/s41467-019-14222-x
• Primary Citation Related Structures: 
  6SCE


• PubMed Abstract: 
  

  The CRISPR system provides adaptive immunity against mobile genetic elements in prokaryotes. On binding invading RNA species, Type III CRISPR systems generate cyclic oligoadenylate (cOA) signalling molecules, potentiating a powerful immune response by activating downstream effector proteins, leading to viral clearance, cell dormancy or death. Here we describe the structure and mechanism of a cOA-activated CRISPR defence DNA endonuclease, CRISPR ancillary nuclease 1 (Can1). Can1 has a unique monomeric structure with two CRISPR associated Rossman fold (CARF) domains and two DNA nuclease-like domains. The crystal structure of the enzyme has been captured in the activated state, with a cyclic tetra-adenylate (cA ₄ ) molecule bound at the core of the protein. cA ₄ binding reorganises the structure to license a metal-dependent DNA nuclease activity specific for nicking of supercoiled DNA. DNA nicking by Can1 is predicted to slow down viral replication kinetics by leading to the collapse of DNA replication forks.

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Organizational Affiliation: 
• Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0DE, UK.
Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. [e-mail].
Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 73.53 kDa 
• Atom Count: 5,394 
• Modeled Residue Count: 618 
• Deposited Residue Count: 642 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	638	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHB155
UniProt
Find proteins for Q53W14 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W14  Go to UniProtKB:  Q53W14

Entity ID: 2
Molecule	Chains	Length	Organism	Image
cyclic oligoadenylate	B	4	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.209 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.37	α = 90
b = 84.52	β = 90
c = 123.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): McMahon, S.A., Zhu, W., Graham, S., White, M.F., Gloster, T.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/R008035/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/S000313/1

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary