cryo-EM structure of Mycobacterium smegmatis Lhr helicase C-terminal domain

UID: 10669

Author(s): Wang, Juncheng*, Warren, Garrett M.*, Shuman, Stewart H.*, Patel, Dinshaw J.* * MSK affiliated

Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes cryogenic electron microscopy data identifying the structure of Mycobacterium smegmatis Lhr helicase C-terminal domain. The main summary display for this entry includes information on the experimental method, validation and macromolecules 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
Visualization and data from the electron microscopy experiment
Accession #: 7LHL
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/pdb7LHL/pdb
Associated Publications: Warren G, Wang J, Patel D, Shuman S. Oligomeric quaternary structure of Escherichia coli and Mycobacterium smegmatis Lhr helicases is nucleated by a novel C-terminal domain composed of five winged-helix modules. Nucleic Acids Research. 2021; 49(7):3876-3887.
Data Type: Analytical Chemistry
Equipment Used: FEI TITAN KRIOS
Electron microscope and imaging robot optimized for high-resolution structural biology.

FEI VITROBOT MARK IV
Vitrobot completely automates the vitrification process
Software Used: 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.
Dataset Format(s): PDF, XML, FASTA, PDB, CIF
Data Tool(s): Electron Microscopy
Dataset Size: 2 KB (FASTA), 331 KB (PDB)

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