9IPU: cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome

PDB ID: 9IPUDownload
MMDB ID: 253173
PDB Deposition Date: 2024/7/11
Updated in MMDB: 2024/10
Experimental Method:
electron microscopy
Resolution: 4.3  Å
Source Organism:
Similar Structures:
Biological Unit for 9IPU: 14-meric; determined by author
Molecular Components in 9IPU
Label Count Molecule
Proteins (12 molecules)
1
Histone H1.0
(Gene symbol: H1-0)
Molecule annotation
2
Histone H3.2
(Gene symbol: H3C14)
Molecule annotation
2
Histone H4
(Gene symbol: H4C9)
Molecule annotation
2
Histone H2A Type 1-b/e
(Gene symbol: H2AC8)
Molecule annotation
2
Histone H2B Type 1-K
(Gene symbol: H2BC12)
Molecule annotation
1
Ubiquitin-conjugating Enzyme E2 D3
(Gene symbol: UBE2D3)
Molecule annotation
1
E3 Ubiquitin-protein Ligase Rnf168
(Gene symbol: RNF168)
Molecule annotation
1
Ubiquitin
(Gene symbol: RPS27A)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (171-mer)
Molecule annotation
1
DNA (171-mer)
Molecule annotation
Chemicals and Non-standard biopolymers (2 molecules)
1
2
ZINC IONZINC ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303