8ZQC | pdb_00008zqc

Cryo-EM structure of Cas12X2 with crRNA and Target DNA

PDB DOI: https://doi.org/10.2210/pdb8ZQC/pdb
NAKB: 8ZQC
EM Map EMD-60382: EMDB EMDataResource

Classification: RNA BINDING PROTEIN/RNA/DNA
Organism(s): unclassified sequences
Expression System: Escherichia coli BL21(DE3), unclassified sequences
Mutation(s): No

Deposited: 2024-06-01 Released: 2025-06-04
Deposition Author(s): Zhang, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of Cas12X2 with crRNA and Target DNA

Zhang, X.

To be published.

Macromolecule Content

Total Structure Weight: 155.16 kDa
Atom Count: 9,680
Modeled Residue Count: 1,029
Deposited Residue Count: 1,097
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas12X2	A	957	unclassified sequences	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
CrRNA	B	56	unclassified sequences
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
TS	C	42	unclassified sequences
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
NTS	D	42	unclassified sequences
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-06-04
Type: Initial release
Version 1.1: 2025-07-23
Changes: Data collection

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.