8XV6: PHD domain of UHRF1

Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119). Determined by X-ray diffraction at 1.6 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 1,686
Mol. weight: 26.36 kDa
Ligands: ZN, SCN
Released: 6 Nov 2024

Explore 8XV6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XV6 contains 13 α-helices and 8 β-strands across 4 chains. 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.

Chains A and C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	318	1	1
α-helix	327-329	3
β-strand	330-332	3	1
α-helix	333	1
β-strand	339-341	3	1
α-helix	348-349	2
α-helix	361-364	4

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	88-89	2
β-strand	90	1	1
α-helix	91-95	5
α-helix	98-112	15

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	90	1	2
α-helix	91-95	5
α-helix	98-112	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A, C	protein	75	Homo sapiens	Q96T88 (AlphaFold model)
Developmental pluripotency-associated protein 3	B, D	protein	35	Mus musculus	Q8QZY3 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8XV6_1 E3 ubiquitin-protein ligase UHRF1 (chains A, C)
GPLGSSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSV
PSEDEWYCPECRNDA

Sequence of entity 2 (B, D), FASTA

>8XV6_2 Developmental pluripotency-associated protein 3 (chains B, D)
KRRVRTLLSVLKDPIAKMRRLVRIEQRQKRLEGNE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10
SCN	Thiocyanate ion	C N S	6

Water and common crystallization additives (GOL) are not listed.

Primary citation

Defining ortholog-specific UHRF1 inhibition by STELLA for cancer therapy. Bai, W., Xu, J., Gu, W. et al. Nat Commun (2025) 16:474-474. DOI 10.1038/s41467-024-55481-7 · 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
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
3SHB 1.8 Å, Crystal Structure of PHD Domain of UHRF1

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