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 9CDB | pdb_00009cdb

CryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in cA6 (partial density) bound form with ATP (partial density).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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

Validation slider image for 9CDB

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 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.

Macromolecule Content 

  • Total Structure Weight: 415.61 kDa 
  • Atom Count: 28,605 
  • Modeled Residue Count: 3,585 
  • Deposited Residue Count: 3,618 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')G [auth H],
H [auth I],
I [auth J]
6Bacteroidales 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: 3.60 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