5M9N: Human TDRD1 extended Tudor domain

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide. Determined by X-ray diffraction at 1.95 Å resolution. Released 16 Nov 2016.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,249
Mol. weight: 50.77 kDa
Ligands: 2MR
Released: 16 Nov 2016

Explore 5M9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M9N contains 20 α-helices and 30 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	479-481	3
β-strand	486	1	1
β-strand	494-504	11	2
β-strand	507-512	6	2
α-helix	513-515	3
α-helix	516-531	16
α-helix	541-542	2
β-strand	546-550	5	3
β-strand	557-567	11	3
β-strand	570-575	6	3
β-strand	581-585	5	3
α-helix	586-588	3
β-strand	589-590	2	3
α-helix	594-597	4
α-helix	600	1
β-strand	601	1	1
β-strand	604-608	5	2
β-strand	611-613	3	4
α-helix	620-630	11
β-strand	635-642	8	2
β-strand	647-653	7	2
β-strand	660-661	2	2
α-helix	662-668	7
β-strand	672-674	3	4

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	479-481	3
β-strand	486	1	5
α-helix	487-488	2
β-strand	494-504	11	6
β-strand	507-512	6	6
α-helix	515-532	18
α-helix	534-535	2
α-helix	541-542	2
β-strand	546-550	5	7
β-strand	557-567	11	7
β-strand	570-575	6	7
β-strand	581-585	5	7
α-helix	586-588	3
β-strand	589-590	2	7
α-helix	594-597	4
α-helix	600	1
β-strand	601	1	5
α-helix	603	1
β-strand	604-608	5	6
β-strand	615	1	8
β-strand	617	1	8
α-helix	620-630	11
β-strand	635-642	8	6
β-strand	647-653	7	6
β-strand	660-661	2	6
α-helix	662-668	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tudor domain-containing protein 1	A, B	protein	220	Homo sapiens	Q9BXT4 (AlphaFold model)
E2F peptide	C	protein	17	Homo sapiens	Q01094 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5M9N_1 Tudor domain-containing protein 1 (chains A, B)
DQSDPEDVGKMTTENNIVVDKSDLIPKVLTLNVGDEFCGVVAHIQTPEDFFCQQLQSGRK
LAELQASLSKYCDQLPPRSDFYPAIGDICCAQFSEDDQWYRASVLAYASEESVLVGYVDY
GNFEILSLMRLCPIIPKLLELPMQAIKCVLAGVKPSLGIWTPEAICLMKKLVQNKIITVK
VVDKLENSSLVELIDKSETPHVSVSKVLLDAGFAVGEQSM

Sequence of entity 2 (C), FASTA

>5M9N_2 E2F peptide (chains C)
SSGPARGRGRHPGKGVK

Ligands and cofactors

ID	Name	Formula	Copies
2MR	N3, N4-dimethylarginine	C8 H18 N4 O2	1

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

Primary citation

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide. Tallant, C., Savitsky, P., Moehlenbrink, J. et al. To be published.

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