5J39: Extended TUDOR domain from TDRD2

Crystal Structure of the extended TUDOR domain from TDRD2. Determined by X-ray diffraction at 1.95 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,166
Mol. weight: 47.54 kDa
Ligands: CAC
Released: 13 Apr 2016

Explore 5J39 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J39 contains 20 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: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	302-305	4
β-strand	307-317	11	1
β-strand	320-325	6	1
α-helix	328-344	17
α-helix	347-349	3
β-strand	359-364	6	2
β-strand	369-378	10	2
α-helix	383	1
β-strand	384-388	5	2
β-strand	394-397	4	2
α-helix	399-401	3
β-strand	403-404	2	2
α-helix	405-406	2
α-helix	407-410	4
α-helix	413-414	2
β-strand	417-421	5	1
β-strand	424-426	3	3
α-helix	433-443	11
β-strand	451-461	11	1
β-strand	464-473	10	1
β-strand	480-481	2	1
α-helix	482-488	7
β-strand	492-494	3	3

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	307-317	11	4
β-strand	320-325	6	4
α-helix	328-344	17
α-helix	347-349	3
β-strand	359-364	6	5
β-strand	369-378	10	5
α-helix	383	1
β-strand	384-388	5	5
β-strand	394-397	4	5
α-helix	399-401	3
β-strand	403-404	2	5
α-helix	405-406	2
α-helix	407-409	3
α-helix	413-414	2
β-strand	417-421	5	4
β-strand	424-426	3	6
α-helix	433-443	11
β-strand	451-459	9	4
β-strand	466-473	8	4
β-strand	480-481	2	4
α-helix	482-488	7
β-strand	492-494	3	6
α-helix	495-496	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tudor and KH domain-containing protein	A, B	protein	208	Homo sapiens	Q9Y2W6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5J39_1 Tudor and KH domain-containing protein (chains A, B)
MHHHHHHSSGRENLYFQGEVYVSASEHPNHFWIQIVGSRSLQLDKLVNEMTQHYENSVPE
DLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFL
SLPFQAIECSLARIAPSGDQWEEEALDEFDRLTHCADWKPLVAKISSYVQTGISTWPKIY
LYDTSNGKKLDIGLELVHKGYAIELPED

Ligands and cofactors

ID	Name	Formula	Copies
CAC	Cacodylate ion	C2 H6 As O2	2

Water and common crystallization additives (UNX) are not listed.

Primary citation

Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2. Zhang, H., Liu, K., Izumi, N. et al. Proc Natl Acad Sci U S A (2017) 114:12483-12488. DOI 10.1073/pnas.1711486114 · PubMed

Other PDB entries of the same protein (UniProt Q9Y2W6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FDR 1.75 Å, Crystal structure of TDRD2
6B57 1.93 Å, tudor in complex with ligand
6PI7 2.8 Å, Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody…
2DIQ Solution structure of the TUDOR domain of Tudor and KH domain containing protein

Browse structure collections

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