4RIQ: DPY-30 dimerization/docking domain

Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI). Determined by X-ray diffraction at 2.23 Å resolution. Released 17 Dec 2014.

Method: X-ray diffraction
Resolution: 2.23 Å
Organism: Homo sapiens
Chains: 24
Atoms: 7,461
Mol. weight: 126.01 kDa
Released: 17 Dec 2014

Explore 4RIQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RIQ contains 81 α-helices and 0 β-strands across 24 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: 4 helices, 0 β-strands

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

Chains B, G, H, J, K, N, P, Q, S and T: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	53-60	8
α-helix	62-75	14
α-helix	80-91	12
α-helix	92-94	3

Chains C, F, I, L, O, R and X: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	506-521	16
α-helix	524-527	4

Chain 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

Chains E and V: 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	92-94	3

Chain M: 3 helices, 0 β-strands

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

Chain U: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	507-521	15
α-helix	524-527	4

Chain Z: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	53-60	8
α-helix	62-75	14
α-helix	80-91	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein dpy-30 homolog	A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, Z	protein	56	Homo sapiens	Q9C005 (AlphaFold model)
Set1/Ash2 histone methyltransferase complex subunit ASH2	C, F, I, L, O, R, U, X	protein	27	Homo sapiens	Q9UBL3 (AlphaFold model)

Sequence of entity 1 (A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, Z), FASTA

>4RIQ_1 Protein dpy-30 homolog (chains A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, Z)
GKVDLQSLPTRAYLDQTVVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN

Sequence of entity 2 (C, F, I, L, O, R, U, X), FASTA

>4RIQ_2 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains C, F, I, L, O, R, U, X)
GAMGSVEHTLADVLYHVETEVENLYFQ

Primary citation

Molecular Basis for DPY-30 Association to COMPASS-like and NURF Complexes. Tremblay, V., Zhang, P., Chaturvedi, C.P. et al. Structure (2014) 22:1821-1830. DOI 10.1016/j.str.2014.10.002 · PubMed

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

3G36 1.2 Å, Crystal structure of the human DPY-30-like C-terminal domain
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
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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