9WXH | pdb_00009wxh

Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state

PDB DOI: https://doi.org/10.2210/pdb9WXH/pdb
EM Map EMD-66346: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Gammaproteobacteria bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-25 Released: 2026-06-24
Deposition Author(s): Mitsuda, Y., Ishikawa, J., Nagahata, N., Hiraizumi, M., Yamashita, K., Nishimasu, H.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 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

Structural mechanism of SAM-AMP synthesis by the type III-D2 CRISPR effector complex

Mitsuda, Y., Sugaya, M., Ishikawa, J., Nagahata, N., Okazaki, S., Hiraizumi, M., Kato, K., Gootenberg, J.S., Abudayyeh, O.O., Osawa, T., Yamashita, K., Nishimasu, H.

To be published.

Macromolecule Content

Total Structure Weight: 307.02 kDa
Atom Count: 20,118
Modeled Residue Count: 2,392
Deposited Residue Count: 2,552
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas10	B	592	Gammaproteobacteria bacterium	Mutation(s): 0 Gene Names: ENJ84_12795

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR type III-associated protein domain-containing protein	C	635	Gammaproteobacteria bacterium	Mutation(s): 0 Gene Names: ENJ84_12800

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TIGR03986 family CRISPR-associated RAMP protein	D	1,235	Gammaproteobacteria bacterium	Mutation(s): 0 Gene Names: ENJ84_12805

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
CRISPR RNA	A	43	Gammaproteobacteria bacterium
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
Cognate target RNA (CTR)	E	47	Gammaproteobacteria bacterium
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], H [auth B], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C]