3DB3: E3 ubiquitin-protein ligase UHRF1

Name: PDB 3DB3: Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide
Published: 2008-09-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Sept 2008.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,237
Mol. weight: 19.72 kDa
Released: 16 Sept 2008

Explore 3DB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DB3 contains 6 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	130	1	1
β-strand	140-144	5	1
β-strand	151-161	11	1
β-strand	182-188	7	1
α-helix	192-194	3
β-strand	196-200	5	1
α-helix	201-203	3
β-strand	204-205	2	1
α-helix	206-208	3
β-strand	211	1	2
α-helix	212-213	2
α-helix	214-216	3
β-strand	222-227	6	2
β-strand	237-248	12	2
β-strand	253-260	8	2
β-strand	265-271	7	2
β-strand	278	1	2
α-helix	279-280	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A	protein	161	Homo sapiens	Q96T88 (AlphaFold model)
Trimethylated histone H3-K9 peptide	B	protein	6		Q71DI3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DB3_1 E3 ubiquitin-protein ligase UHRF1 (chains A)
GMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIY
HVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEIS
RKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGE

Sequence of entity 2 (B), FASTA

>3DB3_2 Trimethylated histone H3-K9 peptide (chains B)
TARKST

Primary citation

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. Nady, N., Lemak, A., Walker, J.R. et al. J Biol Chem (2011) 286:24300-24311. DOI 10.1074/jbc.M111.234104 · PubMed

Other PDB entries of the same protein (UniProt Q96T88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W92 1.3 Å, Human UHRF1 TTD domain
6VYJ 1.39 Å, Human UHRF1 TTD domain in complex with a fragment
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
3ZVZ 1.45 Å, PHD finger of human UHRF1
7FB7 1.45 Å, Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
8XV6 1.6 Å, Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)
6B9M 1.68 Å, Crystal structure of UHRF1 TTD domain in complex with the polybasic region
6IIW 1.7 Å, Crystal structure of human UHRF1 PHD finger in complex with PAF15
3BI7 1.7 Å, Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1
5YYA 1.7 Å, Crystal structure of Tandem Tudor Domain of human UHRF1
6VCS 1.7 Å, SRA domain of UHRF1 in complex with DNA
3FL2 1.75 Å, Crystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1

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