2ZO2: Mouse NP95 SRA domain non-specific DNA complex

Mouse NP95 SRA domain non-specific DNA complex. Determined by X-ray diffraction at 3.09 Å resolution. Released 9 Sept 2008.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Mus musculus
Chains: 3
Atoms: 2,010
Mol. weight: 31.34 kDa
Ligands: PO4
Released: 9 Sept 2008

Explore 2ZO2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZO2 contains 8 α-helices and 10 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 B: 8 helices, 10 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	476	1	1
β-strand	480-484	5	1
α-helix	509-516	8
β-strand	526-527	2	1
α-helix	531-533	3
α-helix	535-536	2
β-strand	537-542	6	1
α-helix	543-545	3
β-strand	557-572	16	1
β-strand	578-586	9	1
α-helix	596-605	10
β-strand	610	1	1
α-helix	615-624	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	B	protein	212	Mus musculus	Q8VDF2 (AlphaFold model)
DNA (5'-d(dapdapdcpdtpdgpdcpdgpdcpdapdgpdtpdt)-3')	D, E	DNA	12

Sequence of entity 1 (B), FASTA

>2ZO2_1 E3 ubiquitin-protein ligase UHRF1 (chains B)
HMPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVD
NGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKP
VRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTR
EGKDRTRQLGLTMQYPEGYLEALANKEKSRKR

Sequence of entity 2 (D, E), FASTA

>2ZO2_2 DNA (5'-D(*DAP*DAP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DTP*DT)-3') (chains D, E)
AACTGCGCAGTT

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Primary citation

The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Hashimoto, H., Horton, J.R., Zhang, X. et al. Nature (2008) 455:826-829. DOI 10.1038/nature07280 · 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
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.
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

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