7VYX | pdb_00007vyx

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 (Depositor), 0.293 (DCC)
R-Value Work:
0.256 (Depositor), 0.256 (DCC)
R-Value Observed:
0.258 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7VYX

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
Modeled Residue Count: 2,668
Deposited Residue Count: 3,000
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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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
UniProt
Find proteins for A0A9X9ZA50 (Parasutterella muris) Explore A0A9X9ZA50 Go to UniProtKB: A0A9X9ZA50
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9X9ZA50
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
sgRNA	C, D	136	Escherichia coli
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Reference Sequence

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

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Molecule	Chains	Length	Organism	Image
Entity ID: 4
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 J [auth B] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	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 (Depositor), 0.293 (DCC)
R-Value Work: 0.256 (Depositor), 0.256 (DCC)
R-Value Observed: 0.258 (Depositor)

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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.