7VYX

Crystal structure of the selenomethionine(SeMet)-derived Cas12c1 (D969A) ternary complex

PDB DOI: https://doi.org/10.2210/pdb7VYX/pdb
NAKB: 7VYX

Classification: RNA BINDING PROTEIN/RNA/DNA
Organism(s): Parasutterella muris, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-15 Released: 2022-11-02
Deposition Author(s): Zhang, B., Lin, J.Y., Perculija, V., OuYang, S.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.292
R-Value Work: 0.256
R-Value Observed: 0.258

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural insights into target DNA recognition and cleavage by the CRISPR-Cas12c1 system

Zhang, B., Lin, J., Perculija, V., Li, Y., Lu, Q., Chen, J., Ouyang, S.

(2022) Nucleic Acids Res 50: 11820-11833

DOI: https://doi.org/10.1093/nar/gkac987

Macromolecule Content

Total Structure Weight: 421.28 kDa
Atom Count: 24,465
Modelled Residue Count: 2,668
Deposited Residue Count: 3,000
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
Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant	A, B	1,310	Parasutterella muris	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
sgRNA	C, D	136	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target DNA strand	E, F	31	Escherichia coli
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
Non-target DNA strand	G, H	23	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B]	I [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.292
R-Value Work: 0.256
R-Value Observed: 0.258
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.127	α = 90
b = 149.85	β = 91.59
c = 173.246	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31770948

Revision History (Full details and data files)

Version 1.0: 2022-11-02
Type: Initial release
Version 1.1: 2023-05-24
Changes: Database references
Version 1.2: 2023-06-14
Changes: Source and taxonomy, Structure summary
Version 1.3: 2024-11-13
Changes: Data collection, Structure summary

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.