Download MendeleyStructural 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
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
- 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 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant | 1,310 | Parasutterella muris | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| sgRNA | 136 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| Target DNA strand | 31 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| Non-target DNA strand | 23 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | I [auth A], J [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| 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 Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-11-02 Deposition Author(s): Zhang, B., Lin, J.Y., Perculija, V., OuYang, S.Y.
| 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
