9C77 | pdb_00009c77

cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in cA4 bound form with ATP.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity.

Baca, C.F.Majumder, P.Hickling, J.H.Ye, L.Teplova, M.Brady, S.F.Patel, D.J.Marraffini, L.A.

(2024) Cell 187: 7183

  • DOI: https://doi.org/10.1016/j.cell.2024.10.002
  • Primary Citation of Related Structures:  
    9C67, 9C68, 9C69, 9C6A, 9C6C, 9C6F, 9C77, 9CDB

  • PubMed Abstract: 

    Type III CRISPR systems provide immunity against genetic invaders through the production of cyclic oligo-adenylate (cA n ) molecules that activate effector proteins that contain CRISPR-associated Rossman fold (CARF) domains. Here, we characterized the function and structure of an effector in which the CARF domain is fused to an adenosine deaminase domain, CRISPR-associated adenosine deaminase 1 (Cad1). We show that upon binding of cA 4 or cA 6 to its CARF domain, Cad1 converts ATP to ITP, both in vivo and in vitro. Cryoelectron microscopy (cryo-EM) structural studies on full-length Cad1 reveal an hexameric assembly composed of a trimer of dimers, with bound ATP at inter-domain sites required for activity and ATP/ITP within deaminase active sites. Upon synthesis of cA n during phage infection, Cad1 activation leads to a growth arrest of the host that prevents viral propagation. Our findings reveal that CRISPR-Cas systems employ a wide range of molecular mechanisms beyond nucleic acid degradation to provide adaptive immunity in prokaryotes.


  • Organizational Affiliation

    Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine deaminase domain-containing protein
A, B, C, D, E
A, B, C, D, E, F
600Bacteroidales bacteriumMutation(s): 0 
Gene Names: DCM62_02910
EC: 3.5.4.4
UniProt
Find proteins for A0A3C0QUR5 (Bacteroidales bacterium)
Explore A0A3C0QUR5 
Go to UniProtKB:  A0A3C0QUR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3C0QUR5
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*AP*A)-3')
G, H, I
4Bacteroidales bacterium
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth B]
N [auth B]
P [auth C]
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth E],
W [auth E],
Y [auth F],
Z [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth F]
L [auth A]
O [auth B]
R [auth C]
U [auth D]
AA [auth F],
L [auth A],
O [auth B],
R [auth C],
U [auth D],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIHGM 129430, NIHGM 145888

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-12-25
    Changes: Data collection, Database references