9OFC | pdb_00009ofc

CryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimers

PDB DOI: https://doi.org/10.2210/pdb9OFC/pdb
EM Map EMD-70428: EMDB EMDataResource
NAKB: 9OFC

Classification: IMMUNE SYSTEM, HYDROLASE
Organism(s): Thermoanaerobaculum aquaticum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-29 Released: 2025-08-20
Deposition Author(s): Zhao, Y., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.17 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Sequential Conformational Activation of a CARF-Fused Adenosine Deaminase by Cyclic Oligoadenylates

Roth, M., Shu, Y., Trasandidou, D., Zhao, Y., van der Oost, J., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 424.68 kDa
Atom Count: 28,970
Modeled Residue Count: 3,642
Deposited Residue Count: 3,762
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated ring nuclease and adenosine deaminase, subunit A	A B E [auth G] F [auth H] I [auth K] A, B, E [auth G], F [auth H], I [auth K], J [auth L]	625	Thermoanaerobaculum aquaticum	Mutation(s): 0 Gene Names: EG19_07865 EC: 3.5.4.4
UniProt
Find proteins for A0A062XY19 (Thermoanaerobaculum aquaticum) Explore A0A062XY19 Go to UniProtKB: A0A062XY19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A062XY19
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
cA4 cleavage product, A2>P	C D G [auth I] H [auth J] K [auth M] C, D, G [auth I], H [auth J], K [auth M], L [auth N]	2	Thermoanaerobaculum aquaticum
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 EA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth G] SDF format, chain W [auth H] SDF format, chain Y [auth K] MOL2 format, chain EA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth G] MOL2 format, chain W [auth H] MOL2 format, chain Y [auth K] mmCIF format, chain EA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth G] mmCIF format, chain W [auth H] mmCIF format, chain Y [auth K]	EA [auth L] M [auth A] O [auth B] Q [auth G] W [auth H] EA [auth L], M [auth A], O [auth B], Q [auth G], W [auth H], Y [auth K]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain EA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth G] Focus chain W [auth H] Focus chain Y [auth K] Interactions & Density Focus chain EA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth G] Focus chain W [auth H] Focus chain Y [auth K]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain FA [auth L] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain T [auth G] SDF format, chain X [auth H] MOL2 format, chain BA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth G] MOL2 format, chain X [auth H] mmCIF format, chain BA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth G] mmCIF format, chain X [auth H]	BA [auth K] FA [auth L] N [auth A] P [auth B] T [auth G] BA [auth K], FA [auth L], N [auth A], P [auth B], T [auth G], X [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain FA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain T [auth G] Focus chain X [auth H] Interactions & Density Focus chain BA [auth K] Focus chain FA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain T [auth G] Focus chain X [auth H]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain CA [auth L] SDF format, chain DA [auth L] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain U [auth H] SDF format, chain V [auth H] SDF format, chain Z [auth K] MOL2 format, chain AA [auth K] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth L] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] MOL2 format, chain Z [auth K] mmCIF format, chain AA [auth K] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth L] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain U [auth H] mmCIF format, chain V [auth H] mmCIF format, chain Z [auth K]	AA [auth K] CA [auth L] DA [auth L] R [auth G] S [auth G] AA [auth K], CA [auth L], DA [auth L], R [auth G], S [auth G], U [auth H], V [auth H], Z [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain R [auth G] Focus chain S [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain R [auth G] Focus chain S [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain Z [auth K]