5VW1: Crystal structure of SpyCas9-sgRNA-AcrIIA4 ternary complex

UID: 10992

Author(s): Yang, Hui*, Patel, Dinshaw J.* * MSK affiliated

Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes x-ray diffraction data identifying the crystal structure of the SpyCas9-sgRNA-AcrIIA4 ternary complex. The main summary display for this entry includes information on the experimental method, protein source, macromolecules and small molecules included in the deposit, and version history and funding identification. Data is provided for download as FASTA sequence format, the Protein Data Bases own PDB format, crystallographic information file (.cif), XML, the EM map, as well as the full validation file in PDF and XML format. Additionally, the PDB provides embedded visualization software to display a 3D view of the protein: PDB's Mol* viewer, NGL viewer, and JSmol. PDB provides protein family and gene product annotations, additional details about the experiment parameters, a Protein Feature Viewer (in the Sequence tab) which displays all available features and alignments of known polymer instances, and a genome view which provides graphical summaries of the correspondences between PDB Entity sequences and genomes.

Subject of Study

Subject(s)

Access via RCSB PDB
Access Restrictions: Free to All
Access Instructions: The RCSB Protein Data Base provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). Sequence, protein structure, EM, and other data can be downloaded in formats specific to the data they contain.
DOI: 10.2210/pdb5VW1/pdb
Associated Publications: Yang H, Patel D. Inhibition mechanism of an anti-CRISPR suppressor AcrIIA4 targeting SpyCas9. Molecular Cell. 2017; 67(1):117-127.e5.
Software Used: HKL-2000
The HKL-2000 program package is based on the extended versions of Denzo, XdisplayF and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important elements are: simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc.

PDB EXTRACT
Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.

PHENIX
A software suite for the automated determination of molecular structures using X-ray crystallography and other methods
Dataset Format(s): XML, FASTA, gzip, PDB, CIF, DSN6, MTX

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