6O7H

Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.

Jia, N., Jones, R., Sukenick, G., Patel, D.J.

(2019) Mol Cell 75: 933-943.e6

  • DOI: 10.1016/j.molcel.2019.06.013
  • Primary Citation of Related Structures:  
    6O73, 6O74, 6O75, 6O78, 6O79, 6O7B, 6O7D, 6O7E, 6O7H, 6O7I

  • PubMed Abstract: 

    • Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA n ) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit ...

    Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA n ) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit. The generated cA n second messenger in turn targets the CARF domain of trans-acting RNase Csm6, triggering its HEPN domain-based RNase activity. We have undertaken cryo-EM studies on multi-subunit Thermococcus onnurineus Csm effector ternary complexes, as well as X-ray studies on Csm1-Csm4 cassette, both bound to substrate (AMPPNP), intermediates (pppA n ), and products (cA n ), to decipher mechanistic aspects of cA n formation and release. A network of intermolecular hydrogen bond alignments accounts for the observed adenosine specificity, with ligand positioning dictating formation of linear pppA n intermediates and subsequent cA n formation by cyclization. We combine our structural results with published functional studies to highlight mechanistic insights into the role of the Csm effector complex in mediating the cA n signaling pathway.

    Organizational Affiliation: 

    Structural Biology Program Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)A791Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: csm1, cas10, TON_0893
EC: 3.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for B6YWB8 (Thermococcus onnurineus (strain NA1))
Explore B6YWB8 
Go to UniProtKB:  B6YWB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWB8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Csm2B188Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0894
UniProt
Find proteins for B6YWB9 (Thermococcus onnurineus (strain NA1))
Explore B6YWB9 
Go to UniProtKB:  B6YWB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWB9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Csm3C, D292Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0895
UniProt
Find proteins for B6YWC0 (Thermococcus onnurineus (strain NA1))
Explore B6YWC0 
Go to UniProtKB:  B6YWC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWC0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Csm4E289Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0896, csm4
UniProt
Find proteins for B6YWC1 (Thermococcus onnurineus (strain NA1))
Explore B6YWC1 
Go to UniProtKB:  B6YWC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWC1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Csm5H [auth F]378Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0897
UniProt
Find proteins for B6YWC2 (Thermococcus onnurineus (strain NA1))
Explore B6YWC2 
Go to UniProtKB:  B6YWC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWC2
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (38-MER)F [auth G]38Thermococcus onnurineus NA1
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
RNA (40-MER)G [auth H]40Thermococcus onnurineus NA1
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 8
MoleculeChainsLengthOrganismImage
Cyclic DNA cA4I [auth K]4synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G
Query on G
Download Ideal Coordinates CCD File 
M [auth H]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth A],
K [auth C],
L [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references