9J9E | pdb_00009j9e

Cryo-EM structure of the type VII CRISPR-Cas14 effector complex

PDB DOI: https://doi.org/10.2210/pdb9J9E/pdb
EM Map EMD-61266: EMDB EMDataResource

Classification: RNA BINDING PROTEIN/RNA
Organism(s): synthetic construct, Spirochaetota bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-22 Released: 2026-03-04
Deposition Author(s): Hiraizumi, M., Yamashita, K., Nishimasu, H.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 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

Cryo-EM structure of type VII CRISPR-Cas14 effector complex

Hiraizumi, M.

To be published.

Macromolecule Content

Total Structure Weight: 539.16 kDa
Atom Count: 28,391
Modeled Residue Count: 3,398
Deposited Residue Count: 4,434
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas5	C	240	Spirochaetota bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas7	D [auth D1] E [auth D2] F [auth D3] G [auth D4] H [auth D5] D [auth D1], E [auth D2], F [auth D3], G [auth D4], H [auth D5], I [auth D6], J [auth D7], K [auth D8]	200	Spirochaetota bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas14	L [auth E1], M [auth E2], N [auth E3], O [auth E4]	609	Spirochaetota bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
crRNA	A	60	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tgRNA	B	98	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth E4] SDF format, chain BA [auth E4] SDF format, chain P [auth C] SDF format, chain Q [auth D1] SDF format, chain R [auth D2] SDF format, chain S [auth D3] SDF format, chain T [auth D4] SDF format, chain U [auth D5] SDF format, chain V [auth D6] SDF format, chain W [auth D7] SDF format, chain X [auth D8] SDF format, chain Y [auth E2] SDF format, chain Z [auth E2] MOL2 format, chain AA [auth E4] MOL2 format, chain BA [auth E4] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D1] MOL2 format, chain R [auth D2] MOL2 format, chain S [auth D3] MOL2 format, chain T [auth D4] MOL2 format, chain U [auth D5] MOL2 format, chain V [auth D6] MOL2 format, chain W [auth D7] MOL2 format, chain X [auth D8] MOL2 format, chain Y [auth E2] MOL2 format, chain Z [auth E2] mmCIF format, chain AA [auth E4] mmCIF format, chain BA [auth E4] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D1] mmCIF format, chain R [auth D2] mmCIF format, chain S [auth D3] mmCIF format, chain T [auth D4] mmCIF format, chain U [auth D5] mmCIF format, chain V [auth D6] mmCIF format, chain W [auth D7] mmCIF format, chain X [auth D8] mmCIF format, chain Y [auth E2] mmCIF format, chain Z [auth E2]	AA [auth E4] BA [auth E4] P [auth C] Q [auth D1] R [auth D2] AA [auth E4], BA [auth E4], P [auth C], Q [auth D1], R [auth D2], S [auth D3], T [auth D4], U [auth D5], V [auth D6], W [auth D7], X [auth D8], Y [auth E2], Z [auth E2]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E4] Focus chain BA [auth E4] Focus chain P [auth C] Focus chain Q [auth D1] Focus chain R [auth D2] Focus chain S [auth D3] Focus chain T [auth D4] Focus chain U [auth D5] Focus chain V [auth D6] Focus chain W [auth D7] Focus chain X [auth D8] Focus chain Y [auth E2] Focus chain Z [auth E2] Interactions & Density Focus chain AA [auth E4] Focus chain BA [auth E4] Focus chain P [auth C] Focus chain Q [auth D1] Focus chain R [auth D2] Focus chain S [auth D3] Focus chain T [auth D4] Focus chain U [auth D5] Focus chain V [auth D6] Focus chain W [auth D7] Focus chain X [auth D8] Focus chain Y [auth E2] Focus chain Z [auth E2]