The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation T in the presence of DnaK chaperone and a model substrate

UID: 10729

Author(s): Yin, Yanting, Li, Huilin

Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes electron microscopy data used to describe the Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation T in the presence of DnaK chaperone and a model substrate. The main summary display for this entry includes information on the experimental method, validation, macromolecules, small molecules included in the deposit, as well as 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 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.

Subject of Study

Subject(s)

Access via PDB
Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 6W6I
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/pdb6W6I/pdb
Associated Publications: Yin Y, Feng X, Yu H, et al. Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system. Cell Reports. 2021; 35(8):109166.
Data Type: Analytical Chemistry
Equipment Used: FEI TITAN KRIOS
Electron microscope and imaging robot optimized for high-resolution structural biology.

GATAN K2 SUMMIT
14.2 Megapixel camera optimized for single particle structural biology, cryo-tomography, plus high-speed dynamic and in-situ electron microscopy.
Software Used: 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.
Dataset Format(s): PDF, XML, FASTA, PDB, CIF, MAP
Data Tool(s): Electron Microscopy
Dataset Size: 523 KB (PDB)

Do you have or know of a dataset that should be added to the catalog? Let us know!