3OMC: Human SND1 extended tudor domain

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s. Determined by X-ray diffraction at 1.77 Å resolution. Released 15 Sept 2010.

Method: X-ray diffraction
Resolution: 1.77 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,790
Mol. weight: 61.41 kDa
Released: 15 Sept 2010

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

Secondary structure: helices and β-sheets

3OMC contains 26 α-helices and 26 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: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	682	1
β-strand	683-690	8	1
β-strand	695-700	6	1
α-helix	701-703	3
α-helix	704-720	17
α-helix	723-725	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	777-778	2	2
α-helix	782-784	3
β-strand	793-798	6	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

Chain B: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	683-690	8	4
β-strand	695-700	6	4
α-helix	701-703	3
α-helix	704-720	17
α-helix	722-723	2
α-helix	724-726	3
α-helix	730-731	2
β-strand	735-739	5	5
β-strand	745-755	11	5
β-strand	758-762	5	5
β-strand	769-772	4	5
α-helix	774-776	3
β-strand	777-779	3	5
α-helix	782-784	3
β-strand	793-798	6	4
β-strand	801-802	2	6
α-helix	803-804	2
α-helix	807-821	15
β-strand	824-832	9	4
α-helix	838	1
β-strand	839-844	6	4
β-strand	850	1	4
α-helix	851-857	7
β-strand	862-863	2	6
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, B	protein	261	Homo sapiens	Q7KZF4 (AlphaFold model)
Synthetic peptide	C, D	protein	8	synthetic construct

Sequence of entity 1 (A, B), FASTA

>3OMC_1 Staphylococcal nuclease domain-containing protein 1 (chains A, B)
AKQKKEKVWAHYEEQPVEEVMPVLEEKERSASYKPVFVTEITDDLHFYVQDVETGTQLEK
LMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNR
EVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLN
VEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSAR
LNLWRYGDFRADDADEFGYSR

Sequence of entity 2 (C, D), FASTA

>3OMC_2 SYNTHETIC PEPTIDE (chains C, D)
TGRARARA

Primary citation

Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Liu, K., Chen, C., Guo, Y. et al. Proc Natl Acad Sci U S A (2010) 107:18398-18403. DOI 10.1073/pnas.1013106107 · PubMed

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
5M9O 1.45 Å, Crystal structure of human SND1 extended Tudor domain in complex with a 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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