3F8I: Mouse UHRF1 SRA domain

Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21. Determined by X-ray diffraction at 2.29 Å resolution. Released 6 Jan 2009.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Mus musculus
Chains: 6
Atoms: 4,313
Mol. weight: 62.51 kDa
Released: 6 Jan 2009

Explore 3F8I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F8I contains 17 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	438-443	6
β-strand	454-457	4	1
β-strand	461-467	7	1
β-strand	475-477	3	1
β-strand	480-484	5	1
β-strand	489	1	2
β-strand	500	1	2
α-helix	508-514	7
β-strand	526-527	2	1
α-helix	531-533	3
α-helix	535-536	2
β-strand	537-542	6	1
α-helix	543-546	4
β-strand	557-572	16	1
β-strand	578-586	9	1
α-helix	591-592	2
α-helix	596-604	9
β-strand	610	1	1
α-helix	615-620	6

Chain B: 8 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
β-strand	489	1	4
β-strand	500	1	4
α-helix	508-514	7
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	615-621	7

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(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3'	D, F	DNA	12
5'-d(dgpdtpdcpdapdgpdcpdgpdcpdapdtpdgpdg)-3'	E, G	DNA	12

Sequence of entity 1 (A, B), FASTA

>3F8I_1 E3 ubiquitin-protein ligase UHRF1 (chains A, B)
HMPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVD
NGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKP
VRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTR
EGKDRTRQLGLTMQYPEGYLEALANKEKSRKR

Sequence of entity 2 (D, F), FASTA

>3F8I_2 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3' (chains D, F)
CCATGCGCTGAC

Sequence of entity 3 (E, G), FASTA

>3F8I_3 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3' (chains E, G)
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:

3FDE 1.41 Å, Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space…
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
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

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