Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes x-ray diffraction data identifying the crystal structure of Sec23a/Sec24a/Sec22 when complexed with 4-phenylbutyric acid in a 50mM soaking. 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, XML, and CIF formats. 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

Homo sapiens

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/pdb5VNN/pdb
Associated Publications: Ma W, Goldberg E, Goldberg J. ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate. eLife. 2017; 6:e26624.
Equipment Used: APS (Advanced Photon Source) Beamline 24-ID-C
Sector 24 utilizes canted insertion devices to provide two independent x-ray sources, one for a variable energy beamline 24-ID-C and another for a fixed energy beamline 24-ID-E (Se peak). Both beamlines are optimized to address challenging cases in macromolecular crystallography such as large complex molecular assemblies, poorly diffracting crystals and microcrystals by providing extremely stable and intense x-ray beams with beam sizes ranging from 5 to 70 microns. The 24-ID-C beamline is equipped with an ALS-style sample auto-mount robotic system for increased productivity and a mini-kappa goniometer head for crystal alignment.

DECTRIS PILATUS3 6M
Hybrid Photon Counting X-ray detector
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.

PHASER
Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods.

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

Data Catalog Record Updated: 2023-11-13

5VNN: Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (50mM soaking)