Cryo-EM structure of CARD8-CARD filament

Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes cryogenic electron microscopy data identifying the cryo-EM structure of CARD8-CARD filament. The main summary display for this entry includes information on the experimental method, validation and macromolecules in the deposit, as well as entry history and funding information. 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 either PDF or XML 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.

The associated EMPIAR Image Set, linked here, includes the 2D tiff images use to develop the 3D modeling.

Subject of Study

Homo sapiens

Subject(s)

Apoptosis

Apoptosis Regulatory Proteins

CARD Signaling Adaptor Proteins

Caspase 1

Caspase Activation and Recruitment Domain

Death Domain Receptor Signaling Adaptor Proteins

Inflammasomes

Neoplasm Proteins

NLR Family, Pyrin Domain-Containing 3 Protein

Access via PDB
Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 6XKJ

Access via EMPIAR
Multi-frame micrographs for the CARD8 CT filament
Accession #: EMPIAR-10567
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.

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images, the raw images used to build a 3D structure. Image sets are available for browsing and download. Accessions are linked to their related PDB and EMDB entries.
DOI: 10.2210/pdb6XKJ/pdb
Associated Publications: Robert Hollingsworth L, David L, Li Y, et al. Ruan J, Sharif H, Fontana P, Orth-He E, Fu T, Bachovchin D, Wu H. Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 inflammasomes. Nature Communications. 2021; 12:189.
Data Type: Analytical Chemistry
Equipment Used: FEI TITAN KRIOS
Electron microscope and imaging robot optimized for high-resolution structural biology.

FEI VITROBOT MARK III
For vitrification of macromolecular complexes and nanocomplexes for cryo-TEM imaging
Software Used: CTFFIND
Program for finding CTFs of electron micrographs

JSmol
HTML5 modality of the Jmol open-source Java viewer for chemical structures in 3D

Mol*
Plugin created by the Protein Data Base to visualize protein structures

NGL
NGL Viewer is a web application for molecular visualization.

PHENIX
A software suite for the automated determination of molecular structures using X-ray crystallography and other methods

REFMAC5
REFMAC now has two ‘modes’: REVIEW which only checks and updates the input model to establish that the geometric restraints can be properly set up, and the standard REFINE mode documented in keywords.

RELION
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

Serial EM
For data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods
Dataset Format(s): PDF, XML, FASTA, PDB, CIF, MAP
Data Tool(s): Electron Microscopy
Dataset Size: 218 KB (FASTA), 199 KB (PDB)

Data Catalog Record Updated: 2021-08-03