8Z3P | pdb_00008z3p

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

PDB DOI: https://doi.org/10.2210/pdb8Z3P/pdb
NAKB: 8Z3P
EM Map EMD-39750: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Limisphaera ngatamarikiensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-15 Released: 2024-12-25
Deposition Author(s): Chen, M.R., Li, Z.X., Xiao, Y.B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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

PubMed: 39666823 Search on PubMed
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, including foreign nucleic acid degradation by CRISPR-Cas systems and DNA and RNA synthesis inhibition through nucleotide pool depletion. Here, we report an antiviral mechanism of type III CRISPR-Cas-regulated adenosine triphosphate (ATP) depletion in which ATP is converted into inosine triphosphate (ITP) by CRISPR-Cas-associated adenosine deaminase (CAAD) upon activation by either cA ₄ or cA ₆, followed by hydrolysis into inosine monophosphate (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 or cA ₆ binds to the CRISPR-associated Rossmann fold (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
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase domain-containing protein	D [auth A] E [auth B] F [auth C] G [auth D] H [auth E] D [auth A], E [auth B], F [auth C], G [auth D], H [auth E], I [auth F]	628	Limisphaera ngatamarikiensis	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6M1RED6
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (5'-R(PAPAPAPAPAPA)-3')	A [auth X], B [auth Y], C [auth Z]	6	Limisphaera ngatamarikiensis
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	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		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A]	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		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C]	O [auth C], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain O [auth C] Focus chain R [auth D]