Description: This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes electron microscopy data identifying the crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD. The main summary display for this entry includes information on the experimental method, validation, macromolecules and 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

Homo sapiens

Subject(s)

Histone Chaperones

Histones

HSP40 Heat-Shock Proteins

Minichromosome Maintenance Complex Component 2

Access via PDB
Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 7ciz
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/pdb7CIZ/pdb
Associated Publications: Hammond C, Bao H, Hendriks I, et al. DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network. Molecular Cell. 2021; 81(12):2533-2548.e9.
Data Type: Analytical Chemistry
Equipment Used: DECTRIS PILATUS3 S 6M
Hybrid Photon Counting X-ray detector

SSRF (Shanghai Synchrotron Radiation Facility) Beamline BL18U1
The scientific goal of BL18U1 is to achieve beam spot of high brightness and photon flux to micrometer level, which can be used to effectively determine the crystal structure of proteins with crystal size as small as 5-10 microns.
Software Used: HKL-3000
The HKL suite is a package of programs intended for the analysis of X-ray diffraction data collected from single crystals, and consists of three programs: XdisplayFfor visualization of the diffraction pattern, Denzofor data reduction and integration, and Scalepackfor merging and scaling of the intensities obtained by Denzoor other programs.

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, PDB, CIF, MTZ, DSN6
Data Tool(s): X-ray crystallography (XRC)
Dataset Size: 662 KB (FASTA), 274 KB (PDB)

Data Catalog Record Updated: 2021-07-15

Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD