2ZKD: SRA domain of mouse Np95

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA. Determined by X-ray diffraction at 1.6 Å resolution. Released 9 Sept 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mus musculus
Chains: 6
Atoms: 5,107
Mol. weight: 61.61 kDa
Released: 9 Sept 2008

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

Secondary structure: helices and β-sheets

2ZKD contains 16 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.

Chains A and B: 8 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	475-476	2	1
β-strand	480-484	5	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
α-helix	543-547	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(dcpdtpdapdcpdcpdgpdgpdapdtpdtpdgpdc)-3')	C, E	DNA	12
DNA (5'-D(DGPDCPDAPDAPDTPDCP(5CM)PDGPDGPDTPDAPDG)-3')	D, F	DNA	12
E3 ubiquitin-protein ligase UHRF1	A, B	protein	210	Mus musculus	Q8VDF2 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>2ZKD_1 DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3') (chains C, E)
CTACCGGATTGC

Sequence of entity 2 (D, F), FASTA

>2ZKD_2 DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3') (chains D, F)
GCAATCCGGTAG

Sequence of entity 3 (A, B), FASTA

>2ZKD_3 E3 ubiquitin-protein ligase UHRF1 (chains A, B)
SGMACVGRTTECTIVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAY
SLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINE
KGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYL
LRRDDTEPEPWTREGKDRTRQLGLTMQYPE

Primary citation

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Arita, K., Ariyoshi, M., Tochio, H. et al. Nature (2008) 455:818-821. DOI 10.1038/nature07249 · 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…
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

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