6IIW: Human UHRF1 PHD finger

Crystal structure of human UHRF1 PHD finger in complex with PAF15. Determined by X-ray diffraction at 1.7 Å resolution. Released 9 Oct 2019.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 699
Mol. weight: 9.53 kDa
Ligands: ZN
Released: 9 Oct 2019

Explore 6IIW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IIW contains 3 α-helices and 4 β-strands across 2 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.

Chain A: 3 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

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A	protein	68	Homo sapiens	Q96T88 (AlphaFold model)
PCNA-associated factor	B	protein	10	Homo sapiens	Q15004 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6IIW_1 E3 ubiquitin-protein ligase UHRF1 (chains A)
GPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEW
YCPECRND

Sequence of entity 2 (B), FASTA

>6IIW_2 PCNA-associated factor (chains B)
VRTKADSVPG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nishiyama, A., Mulholland, C.B., Bultmann, S. et al. Nat Commun (2020) 11:1222-1222. DOI 10.1038/s41467-020-15006-4 · 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
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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