5M9O: Human SND1 extended Tudor domain

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide. Determined by X-ray diffraction at 1.45 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,921
Mol. weight: 26.39 kDa
Released: 7 Dec 2016

Explore 5M9O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M9O contains 12 α-helices and 13 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 A: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	683-690	8	1
β-strand	695-700	6	1
α-helix	701-703	3
α-helix	704-720	17
α-helix	722-724	3
β-strand	735-739	5	2
β-strand	745-755	11	2
β-strand	758-763	6	2
β-strand	769-772	4	2
α-helix	774-776	3
β-strand	777-779	3	2
α-helix	780-781	2
α-helix	782-784	3
β-strand	794-798	5	1
β-strand	801-802	2	3
α-helix	803-804	2
α-helix	807-821	15
β-strand	824-832	9	1
β-strand	839-844	6	1
β-strand	850	1	1
α-helix	851-857	7
β-strand	862-863	2	3
α-helix	869-871	3
α-helix	872-887	16
α-helix	891-893	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Staphylococcal nuclease domain-containing protein 1	A	protein	224	Homo sapiens	Q7KZF4 (AlphaFold model)
E2F peptide	B	protein	9	Homo sapiens	Q01094 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5M9O_1 Staphylococcal nuclease domain-containing protein 1 (chains A)
ERSASYKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPRRGEFC
IAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEY
AFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLV
KEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRYGDFRA

Sequence of entity 2 (B), FASTA

>5M9O_2 E2F peptide (chains B)
ARGRGRHPG

Primary citation

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide. Tallant, C., Savitsky, P., Moehlenbrink, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q7KZF4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HQX 1.42 Å, Crystal structure of human P100 tudor domain conserved region
3OMC 1.77 Å, Structure of human SND1 extended tudor domain in complex with the symmetrically…
3OMG 1.85 Å, Structure of human SND1 extended tudor domain in complex with the symmetrically…
3BDL 1.9 Å, Crystal structure of a truncated human Tudor-SN
2HQE 2.0 Å, Crystal structure of human P100 Tudor domain: Large fragment
2O4X 2.0 Å, Crystal structure of human P100 tudor domain
7KNW 2.65 Å, Crystal structure of SND1 in complex with C-26-A2
7KNX 2.7 Å, Crystal structure of SND1 in complex with C-26-A6
4QMG 2.7 Å, The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions
2E6N Solution structure of the TUDOR domain of Staphylococcal nuclease domain-containing…

Browse structure collections

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