3G36: Human DPY-30-like C-terminal domain

Crystal structure of the human DPY-30-like C-terminal domain. Determined by X-ray diffraction at 1.2 Å resolution. Released 30 Jun 2009.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,017
Mol. weight: 25.81 kDa
Ligands: HEZ, DTV, DTT, DTU
Released: 30 Jun 2009

Explore 3G36 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3G36 contains 19 α-helices and 0 β-strands across 4 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	48-50	3
α-helix	53-58	6
α-helix	62-75	14
α-helix	80-91	12
α-helix	92-95	4

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	48-50	3
α-helix	53-60	8
α-helix	62-75	14
α-helix	80-95	16

Chains C and D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	48-50	3
α-helix	53-60	8
α-helix	62-75	14
α-helix	80-91	12
α-helix	92-95	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein dpy-30 homolog	A, B, C, D	protein	55	Homo sapiens	Q9C005 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3G36_1 Protein dpy-30 homolog (chains A, B, C, D)
KVDLQSLPTRAYLDQTVVPILLQGMAVLAKERPPNPIEFLASYLLKNKAQFEDRN

Ligands and cofactors

ID	Name	Formula	Copies
HEZ	Hexane-1,6-diol	C6 H14 O2	1
DTV	(2S,3S)-1,4-dimercaptobutane-2,3-diol	C4 H10 O2 S2	1
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1
DTU	(2R,3S)-1,4-dimercaptobutane-2,3-diol	C4 H10 O2 S2	1

Primary citation

Crystal structure of the C-terminal domain of human DPY-30-like protein: A component of the histone methyltransferase complex. Wang, X., Lou, Z., Dong, X. et al. J Mol Biol (2009) 390:530-537. DOI 10.1016/j.jmb.2009.05.061 · PubMed

Other PDB entries of the same protein (UniProt Q9C005 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4RT4 2.0 Å, Crystal structure of Dpy30 complexed with Bre2
4RTA 2.12 Å, Cystal structure of the Dpy30 for MLL/SET1 COMPASS H3K4 trimethylation
4RIQ 2.23 Å, Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L…
6E2H 2.24 Å, Crystal structure of human Ash2L (SPRY domain and SDI motif) in complex with full length…
9YM8 3.43 Å, State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub…
9YMF 3.45 Å, State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with…
9YL3 3.5 Å, State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac
9YLE 3.63 Å, State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac
9YLY 3.77 Å, MLL4FC bound to a nucleosome with p53 RE
7UD5 4.25 Å, Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome
6PWV 6.2 Å, Cryo-EM structure of MLL1 core complex bound to the nucleosome

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