9YYG | pdb_00009yyg

AI-generated RNA-guided nuclease TAM-bound state

PDB DOI: https://doi.org/10.2210/pdb9YYG/pdb
EM Map EMD-73644: EMDB EMDataResource
NAKB: 9YYG

Classification: RNA BINDING PROTEIN
Organism(s): synthetic construct, Deinococcus radiodurans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-29 Released: 2026-07-15
Deposition Author(s): Skopintsev, P., Esain-Garcia, I., Doudna, J.
Funding Organization(s): National Science Foundation (NSF, United States), Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YYG

This is version 1.1 of the entry. See complete history.

Literature

Structure and evolution-guided design of minimal RNA-guided nucleases

Skopintsev, P., Esain-Garcia, I., DeTurk, E.C., Yoon, P.H., Zhou, Z., Weiss, T., Kamalu, M., Chamraj, A., Loi, K.J., Langeberg, C.J., Boger, R.S., Nisonoff, H., Karp, H.M., Chen, L.X., Shi, H., Vohra, K., Banfield, J.F., Cate, J.H.D., Jacobsen, S.E., Doudna, J.A.

(2026) Science 393: 313-318

DOI: https://doi.org/10.1126/science.aed6123

Macromolecule Content

Total Structure Weight: 94.4 kDa
Atom Count: 5,410
Modeled Residue Count: 455
Deposited Residue Count: 557
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AI-designed RNA-guided nuclease	A	408	synthetic construct	Mutation(s): 0 EC: 3.1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (116-MER)	B	132	Deinococcus radiodurans
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (5'-D(GPGPTPTPGPAPTPC)-3')	C	8	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 4
DNA (5'-D(APCPAPTPCPAPAPCP*C)-3')	D	9	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3.0
MODEL REFINEMENT	PHENIX	1.21.1-5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-15

Deposition Author(s):

Esain-Garcia, I.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE 2334027
Swiss National Science Foundation	Switzerland	P500PB_214418

Revision History (Full details and data files)

Version 1.0: 2026-07-15
Type: Initial release
Version 1.1: 2026-07-22
Changes: Data collection, Database references

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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.