8PHB

Crystal structure of apo Cami1

• PDB DOI: https://doi.org/10.2210/pdb8PHB/pdb

• Classification: HYDROLASE
• Organism(s): Allochromatium vinosum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-19 Released: 2023-12-13 
• Deposition Author(s): Tamulaitiene, G., Tamulaitis, G., Mogila, I., Keda, K.
• Funding Organization(s): Research Council of Lithuania

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling.

Mogila, I., Tamulaitiene, G., Keda, K., Timinskas, A., Ruksenaite, A., Sasnauskas, G., Venclovas, C., Siksnys, V., Tamulaitis, G.

(2023) Science 382: 1036-1041

• PubMed: 38033086 
• DOI: https://doi.org/10.1126/science.adj2107
• Primary Citation of Related Structures:  
  8PHB, 8PHJ


• PubMed Abstract: 
  

  Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cA _n ) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cA _n -dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA ₄ ), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA ₄ complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins.

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Organizational Affiliation: 

Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 91.81 kDa 
• Atom Count: 6,356 
• Modelled Residue Count: 751 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein, APE2256 family	A, B	406	Allochromatium vinosum	Mutation(s): 0  Gene Names: Alvin_3127
UniProt
Find proteins for D3RW14 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RW14  Go to UniProtKB:  D3RW14

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.238	α = 90
b = 90.428	β = 99.56
c = 65.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
SHELX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Tamulaitiene, G., Tamulaitis, G., Mogila, I., Keda, K.

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Funding Organization	Location	Grant Number
Research Council of Lithuania	Lithuania	S-MIP-22-09

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Database references