3FDE: Mouse UHRF1 SRA domain

Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution. Determined by X-ray diffraction at 1.41 Å resolution. Released 6 Jan 2009.

Method: X-ray diffraction
Resolution: 1.41 Å
Organism: Mus musculus
Chains: 6
Atoms: 5,159
Mol. weight: 63.97 kDa
Released: 6 Jan 2009

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

Secondary structure: helices and β-sheets

3FDE contains 18 α-helices and 24 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: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	425-426	2
β-strand	434-435	2	1
α-helix	438-444	7
β-strand	454-457	4	1
β-strand	461-467	7	1
β-strand	475-476	2	1
β-strand	480-484	5	1
α-helix	485	1
β-strand	489	1	2
β-strand	500	1	2
α-helix	508-515	8
β-strand	526-527	2	1
α-helix	531-533	3
α-helix	535-536	2
β-strand	537-542	6	1
β-strand	557-572	16	1
β-strand	578-586	9	1
α-helix	591-592	2
α-helix	596-605	10
β-strand	610	1	1
α-helix	615-622	8

Chain B: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	425-426	2
β-strand	434-435	2	3
α-helix	438-443	6
β-strand	454-457	4	3
β-strand	461-467	7	3
β-strand	475-476	2	3
β-strand	480-484	5	3
α-helix	485	1
β-strand	489	1	4
β-strand	500	1	4
α-helix	508-515	8
β-strand	526-527	2	3
α-helix	531-533	3
β-strand	537-542	6	3
α-helix	543-547	5
β-strand	557-572	16	3
β-strand	578-586	9	3
α-helix	591-592	2
α-helix	596-604	9
β-strand	610	1	3
α-helix	615-620	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A, B	protein	212	Mus musculus	Q8VDF2 (AlphaFold model)
5'-D(CPCPAPTPGP(5CM)PGPCPTPGPAPC)-3'	C, D	DNA	12
5'-d(gptpcpapgpcpgpcpaptpgpg)-3'	E, F	DNA	12

Sequence of entity 1 (A, B), FASTA

>3FDE_1 E3 ubiquitin-protein ligase UHRF1 (chains A, B)
HMPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVD
NGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKP
VRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTR
EGKDRTRQLGLTMQYPEGYLEALANKEKSRKR

Sequence of entity 2 (C, D), FASTA

>3FDE_2 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3' (chains C, D)
CCATGCGCTGAC

Sequence of entity 3 (E, F), FASTA

>3FDE_3 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3' (chains E, F)
GTCAGCGCATGG

Primary citation

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Hashimoto, H., Horton, J.R., Zhang, X. et al. Epigenetics (2009) 4:8-14. PubMed

Other PDB entries of the same protein (UniProt Q8VDF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZKD 1.6 Å, Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
2ZKG 1.77 Å, Crystal structure of unliganded SRA domain of mouse Np95
2ZO1 1.96 Å, Mouse NP95 SRA domain DNA specific complex 2
3F8J 1.99 Å, Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group…
2ZO0 2.19 Å, mouse NP95 SRA domain DNA specific complex 1
3F8I 2.29 Å, Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group…
2ZKF 2.55 Å, Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
2ZKE 2.6 Å, Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
6M2V 3.0 Å, Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA.
2ZO2 3.09 Å, Mouse NP95 SRA domain non-specific DNA complex
24MC 3.4 Å, Structure of oocyte cytoplasmic lattices
12DL 3.5 Å, Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs

Browse structure collections

About this viewer

MolViewer shows 3FDE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.