7N3O

Cryo-EM structure of the Cas12k-sgRNA complex

PDB DOI: https://doi.org/10.2210/pdb7N3O/pdb
NAKB: 7N3O
EM Map EMD-24142: EMDB EMDataResource

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Scytonema hofmannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-06-01 Released: 2021-09-01
Deposition Author(s): Chang, L., Li, Z., Xiao, R., Wang, S., Han, R.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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

Structural basis of target DNA recognition by CRISPR-Cas12k for RNA-guided DNA transposition.

Xiao, R., Wang, S., Han, R., Li, Z., Gabel, C., Mukherjee, I.A., Chang, L.

(2021) Mol Cell 81: 4457-4466.e5

PubMed: 34450043 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.molcel.2021.07.043
Primary Citation of Related Structures:
7N3O, 7N3P

PubMed Abstract:
The type V-K CRISPR-Cas system, featured by Cas12k effector with a naturally inactivated RuvC domain and associated with Tn7-like transposon for RNA-guided DNA transposition, is a promising tool for precise DNA insertion. To reveal the mechanism underlying target DNA recognition, we determined a cryoelectron microscopy (cryo-EM) structure of Cas12k from cyanobacteria Scytonema hofmanni in complex with a single guide RNA (sgRNA) and a double-stranded target DNA. Coupled with mutagenesis and in vitro DNA transposition assay, our results revealed mechanisms for the recognition of the GGTT protospacer adjacent motif (PAM) sequence and the structural elements of Cas12k critical for RNA-guided DNA transposition. These structural and mechanistic insights should aid in the development of type V-K CRISPR-transposon systems as tools for genome editing.

Organizational Affiliation

Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.

Macromolecule Content

Total Structure Weight: 158.54 kDa
Atom Count: 8,295
Modelled Residue Count: 676
Deposited Residue Count: 904
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas12k	A	639	Scytonema hofmannii	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: 2
Molecule	Chains	Length	Organism	Image
Single guide RNA	B	265	Scytonema hofmannii
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-01
Type: Initial release
Version 1.1: 2022-03-16
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.