9UBO | pdb_00009ubo

The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5

PDB DOI: https://doi.org/10.2210/pdb9UBO/pdb
EM Map EMD-64013: EMDB EMDataResource
NAKB: 9UBO

Classification: HYDROLASE/RNA
Organism(s): Thermoanaerobaculum aquaticum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-03 Released: 2026-04-15
Deposition Author(s): Kong, J.P., Wu, W.Q., Li, Z.X., Xiao, Y.B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UBO

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

Literature

The structure of type III CRISPR-associated deaminase

Kong, J.P., Wu, W.Q., Li, Z.X., Xiao, Y.B.

To be published.

Macromolecule Content

Total Structure Weight: 431.34 kDa
Atom Count: 28,042
Modeled Residue Count: 3,531
Deposited Residue Count: 3,804
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adenosine deaminase	A B [auth D] F [auth B] G [auth C] H [auth E] A, B [auth D], F [auth B], G [auth C], H [auth E], I [auth F]	631	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A062XY19
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R(PAPAPAPAPAPA)-3')	C [auth X], D [auth Y], E [auth Z]	6	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 Y [auth F] SDF format, chain V [auth E] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain M [auth D] SDF format, chain J [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth D] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth D] mmCIF format, chain J [auth A]	J [auth A] M [auth D] P [auth B] S [auth C] V [auth E] J [auth A], M [auth D], P [auth B], S [auth C], V [auth E], Y [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain M [auth D] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth D] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth E] Focus chain Y [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth D] SDF format, chain K [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth D] MOL2 format, chain K [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth D] mmCIF format, chain K [auth A]	K [auth A] N [auth D] Q [auth B] T [auth C] W [auth E] K [auth A], N [auth D], Q [auth B], T [auth C], W [auth E], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth D] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain K [auth A] Focus chain N [auth D] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth E] Focus chain Z [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain O [auth D] SDF format, chain L [auth A] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth A] mmCIF format, chain AA [auth F]	AA [auth F] L [auth A] O [auth D] R [auth B] U [auth C] AA [auth F], L [auth A], O [auth D], R [auth B], U [auth C], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain L [auth A] Focus chain O [auth D] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain L [auth A] Focus chain O [auth D] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82473977

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.