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 H4K20me3. 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 #: 7lmk
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/pdb7LMK/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: ADSC Quantum 315 r
Crystallization and X-ray analysis

APS(Advanced Photon Source) Beamline 24-ID-E
A synchrotron machine exists to accelerate electrons to extremely high energy and then make them change direction periodically. The resulting X-rays are emitted as dozens of thin beams, each directed toward a beamline next to the accelerator.
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.

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.

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: 343 bytes (FASTA), 230 KB (PDB)

Data Catalog Record Updated: 2021-07-06

Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3