8Z3P | pdb_00008z3p

The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, fully activated


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Z3P

This is version 1.1 of the entry. See complete history

Literature

Antiviral signaling of a type III CRISPR-associated deaminase.

Li, Y.Li, Z.Yan, P.Hua, C.Kong, J.Wu, W.Cui, Y.Duan, Y.Li, S.Li, G.Ji, S.Chen, Y.Zhao, Y.Yang, P.Hu, C.Lu, M.Chen, M.Xiao, Y.

(2025) Science 387: eadr0393-eadr0393

  • DOI: https://doi.org/10.1126/science.adr0393
  • Primary Citation Related Structures: 
    8Z3K, 8Z3P, 8Z3R, 8Z40

  • PubMed Abstract: 

    Prokaryotes have evolved diverse defense strategies against viral infection, such as foreign nucleic acid degradation by CRISPR-Cas systems and DNA/RNA synthesis inhibition via nucleotide pool depletion. Here, we report an antiviral mechanism of type III CRISPR-Cas-regulated ATP depletion, where ATP is converted into ITP by CRISPR-Cas-associated adenosine deaminase (CAAD) upon activation by either cA 4 or cA 6 , followed by hydrolysis into IMP by Nudix hydrolase, ultimately resulting in cell growth arrest. The cryo-electron microscopy structures of CAAD in its apo and activated forms, together with biochemical evidence, revealed how cA 4 /cA 6 binds to the CARF domain and abrogates CAAD autoinhibition, inducing substantial conformational changes that reshape the structure of CAAD and induce its deaminase activity. Our results reveal the mechanism of a CRISPR-Cas-regulated ATP depletion antiviral strategy.


  • Organizational Affiliation
    • Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 428.67 kDa 
  • Atom Count: 29,494 
  • Modeled Residue Count: 3,705 
  • Deposited Residue Count: 3,786 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenosine deaminase domain-containing protein628Limisphaera ngatamarikiensisMutation(s): 0 
Gene Names: G4L39_03315
EC: 3.5.4.4
UniProt
Find proteins for A0A6M1RED6 (Limisphaera ngatamarikiensis)
Explore A0A6M1RED6 
Go to UniProtKB:  A0A6M1RED6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M1RED6
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')A [auth X],
B [auth Y],
C [auth Z]
6Limisphaera ngatamarikiensis
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
N [auth C]
Q [auth D]
T [auth E]
J [auth A],
L [auth B],
N [auth C],
Q [auth D],
T [auth E],
V [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A]
M [auth B]
P [auth C]
S [auth D]
U [auth E]
K [auth A],
M [auth B],
P [auth C],
S [auth D],
U [auth E],
W [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
O [auth C],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Data collection, Database references