7Y9X | pdb_00007y9x

Structure of the Cas7-11-Csx29-guide RNA complex

• PDB DOI: https://doi.org/10.2210/pdb7Y9X/pdb
• NAKB: 7Y9X
• EM Map EMD-33695: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Desulfonema ishimotonii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-06-26 Released: 2022-11-09 
• Deposition Author(s): Kato, K., Okazaki, S., Ishikawa, J., Isayama, Y., Nishizawa, T., Nishimasu, H.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease.

Kato, K., Okazaki, S., Schmitt-Ulms, C., Jiang, K., Zhou, W., Ishikawa, J., Isayama, Y., Adachi, S., Nishizawa, T., Makarova, K.S., Koonin, E.V., Abudayyeh, O.O., Gootenberg, J.S., Nishimasu, H.

(2022) Science 378: 882-889

• PubMed: 36423304 
• DOI: https://doi.org/10.1126/science.add7347
• Primary Citation Related Structures: 
  7Y9X, 7Y9Y, 8GS2


• PubMed Abstract: 
  

  The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA (tgRNA), and demonstrate that tgRNA binding induces conformational changes in Csx29. Biochemical experiments revealed tgRNA-dependent cleavage of the accessory protein Csx30 by Csx29. Reconstitution of the system in bacteria showed that Csx30 cleavage yields toxic protein fragments that cause growth arrest, which is regulated by Csx31. Csx30 binds Csx31 and the associated sigma factor RpoE (RNA polymerase, extracytoplasmic E), suggesting that Csx30-mediated RpoE inhibition modulates the cellular response to infection. We engineered the Cas7-11-Csx29-Csx30 system for programmable RNA sensing in mammalian cells. Overall, the Cas7-11-Csx29 effector is an RNA-dependent nuclease-protease.

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Organizational Affiliation: 
• Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Graduate School of Medical Life Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 286.32 kDa 
• Atom Count: 18,662 
• Modeled Residue Count: 2,230 
• Deposited Residue Count: 2,406 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHAT domain-containing protein	A [auth B]	751	Desulfonema ishimotonii	Mutation(s): 0  Gene Names: DENIS_1081
UniProt
Find proteins for A0A401FT52 (Desulfonema ishimotonii) Explore A0A401FT52  Go to UniProtKB:  A0A401FT52

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated RAMP family protein	B [auth A]	1,617	Desulfonema ishimotonii	Mutation(s): 3  Gene Names: DENIS_1082
UniProt
Find proteins for A0A401FT36 (Desulfonema ishimotonii) Explore A0A401FT36  Go to UniProtKB:  A0A401FT36

Entity ID: 3
Molecule	Chains	Length	Organism	Image
crRNA	C [auth R]	38	Desulfonema ishimotonii

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Kato, K., Okazaki, S., Ishikawa, J., Isayama, Y., Nishizawa, T., Nishimasu, H.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2022-12-07
  Changes: Database references
• Version 1.2: 2024-07-03
  Changes: Data collection