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Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2

UID: 10657

Author(s): Ren, Wendan, Song, Jikui

Description
This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes x-ray diffraction data used for modeling the crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2. The main summary display for this entry includes information on the experimental data, validation, macromolecules, small molecules, 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, DSN6 Maps, MTZ Map Coefficients, 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
Bos taurus
Homo sapiens
Subject(s)
DNA (Cytosine-5-)-Methyltransferase 1
Histones
Methyltransferases
Repressor Proteins
Access via PDB

Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 7LMM

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/pdb7LMM/pdb
Associated Publications
Ren W, Fan H, Grimm S, et al. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nature Communications. 2021; 12:2490.
Data Type
Analytical Chemistry
Equipment Used
PILATUS3 S 6M

X-Ray detector

Stanford Synchroton Radiation Lightsource (SSRL) BEAMLINE BL9-2

Beam line 9-2 is a wiggler end station dedicated for monochromatic, high-throughput and high-resolution macromolecular crystallography and optimized for SAD and MAD experiments

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 Tool(s)
X-ray crystallography (XRC)
Dataset Size
380 bytes (FASTA), 233 KB (PDB)
Data Catalog Record Updated
2021-07-06