6M2V: UHRF1 SRA

Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA. Determined by X-ray diffraction at 3.0 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: synthetic construct, Mus musculus
Chains: 4
Atoms: 3,558
Mol. weight: 55.68 kDa
Released: 13 Jan 2021

Explore 6M2V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M2V contains 19 α-helices and 20 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	425-426	2
β-strand	434-435	2	2
α-helix	438-444	7
β-strand	454-457	4	2
β-strand	461-467	7	2
β-strand	475-476	2	2
β-strand	480-484	5	2
α-helix	508-516	9
β-strand	526-527	2	2
α-helix	531-533	3
α-helix	535-536	2
β-strand	537-542	6	2
α-helix	543-548	6
β-strand	557-571	15	2
β-strand	579-586	8	2
α-helix	591-592	2
α-helix	596-605	10
β-strand	610	1	2
α-helix	615-624	10

Chain B: 10 helices, 10 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	476	1	1
β-strand	480-484	5	1
α-helix	509-515	7
β-strand	527	1	1
α-helix	531-533	3
α-helix	535-536	2
β-strand	537-542	6	1
α-helix	543-547	5
β-strand	557-571	15	1
β-strand	579-586	8	1
α-helix	591-592	2
α-helix	596-604	9
β-strand	609-610	2	1
α-helix	611-612	2
α-helix	615-619	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-D(TPCPAPCPGP(5CM)PTPGPCPGPTPGP*A)-3')	C, D	DNA	13	synthetic construct
E3 ubiquitin-protein ligase UHRF1	A, B	protein	212	Mus musculus	Q8VDF2 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>6M2V_1 DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3') (chains C, D)
TCACGCTGCGTGA

Sequence of entity 2 (A, B), FASTA

>6M2V_2 E3 ubiquitin-protein ligase UHRF1 (chains A, B)
IVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVD
NGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKP
VRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTR
EGKDRTRQLGLTMQYPEGYLEALANKEKSRKR

Primary citation

Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Abhishek, S., Nakarakanti, N.K., Deeksha, W. et al. Int J Biol Macromol (2021) 170:514-522. DOI 10.1016/j.ijbiomac.2020.12.149 · 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
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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