7W6L: MLL3-RBBP5-ASH2L

The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide. Determined by X-ray diffraction at 2.26 Å resolution. Released 7 Sept 2022.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 7
Atoms: 5,944
Mol. weight: 86.55 kDa
Ligands: ZN, SAH
Released: 7 Sept 2022

Explore 7W6L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W6L contains 22 α-helices and 68 β-strands across 7 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: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	289-294	6	1
β-strand	299-300	2	2
β-strand	306-308	3	2
β-strand	314-318	5	1
β-strand	322	1	3
β-strand	325-335	11	2
β-strand	341-347	7	1
β-strand	363-367	5	1
α-helix	369-371	3
β-strand	372-375	4	1
β-strand	378-381	4	1
β-strand	391-398	8	2
β-strand	446-451	6	2
β-strand	454-461	8	2
α-helix	463-465	3
β-strand	468	1	3
β-strand	469-475	7	1
β-strand	479-483	5	2
β-strand	498-499	2	2
α-helix	500-502	3

Chain B: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	289-294	6	4
β-strand	299-300	2	5
β-strand	306-308	3	5
β-strand	314-318	5	4
β-strand	322	1	6
β-strand	325-335	11	5
β-strand	341-347	7	4
β-strand	363-367	5	4
β-strand	373-375	3	4
β-strand	378-380	3	4
β-strand	391-398	8	5
α-helix	399-401	3
β-strand	446-451	6	5
β-strand	454-461	8	5
α-helix	463-464	2
β-strand	468	1	6
β-strand	469-475	7	4
β-strand	479-483	5	5
β-strand	498-499	2	5
α-helix	500-502	3

Chain C: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4758-4766	9
α-helix	4769-4771	3
β-strand	4773-4777	5	7
β-strand	4783-4787	5	7
β-strand	4791	1	8
β-strand	4796-4800	5	9
β-strand	4802-4806	5	10
α-helix	4807-4819	13
β-strand	4826-4828	3	10
β-strand	4833-4841	9	10
α-helix	4843-4846	4
α-helix	4847	1
β-strand	4848-4849	2	11
β-strand	4855-4862	8	9
β-strand	4865-4872	8	9
β-strand	4876	1	8
α-helix	4880	1
β-strand	4881	1	7
α-helix	4882	1
β-strand	4883-4884	2	11
α-helix	4888-4890	3
β-strand	4898	1	12
β-strand	4909	1	12

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	337-338	2	10
β-strand	343-344	2	10

Chain E: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4758-4766	9
α-helix	4769-4771	3
β-strand	4773-4777	5	13
β-strand	4783-4787	5	13
β-strand	4791	1	14
β-strand	4796-4800	5	15
β-strand	4803-4806	4	16
α-helix	4807-4819	13
α-helix	4822-4824	3
β-strand	4826-4828	3	16
β-strand	4833-4836	4	16
α-helix	4843-4846	4
α-helix	4847	1
β-strand	4848-4849	2	17
β-strand	4855-4860	6	15
β-strand	4867-4872	6	15
β-strand	4876	1	14
α-helix	4880	1
β-strand	4881	1	13
α-helix	4882	1
β-strand	4883-4884	2	17
β-strand	4897-4898	2	18
β-strand	4909-4910	2	18

Chain F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	343-344	2	16

Chain M: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Set1/Ash2 histone methyltransferase complex subunit ASH2	A, B	protein	184	Homo sapiens	Q9UBL3 (AlphaFold model)
Histone-lysine N-methyltransferase 2C	C, E	protein	159	Homo sapiens	Q8NEZ4
Retinoblastoma-binding protein 5	D, F	protein	27	Homo sapiens	Q15291 (AlphaFold model)
Histone H3.3C	M	protein	9	Homo sapiens	Q6NXT2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7W6L_1 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains A, B)
SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARL
GWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTIS
GRGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPM
SDMG

Sequence of entity 2 (C, E), FASTA

>7W6L_2 Histone-lysine N-methyltransferase 2C (chains C, E)
GPLGSKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANR
KEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVVTFERGHKIIISS
SRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN

Sequence of entity 3 (D, F), FASTA

>7W6L_3 Retinoblastoma-binding protein 5 (chains D, F)
SAFAPDFKELDENVEYEERESEFDIED

Sequence of entity 4 (M), FASTA

>7W6L_4 Histone H3.3C (chains M)
ARTKQTARK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Structural basis for product specificities of MLL family methyltransferases. Li, Y., Zhao, L., Zhang, Y. et al. Mol Cell (2022) 82:3810-3825.e8. DOI 10.1016/j.molcel.2022.08.022 · PubMed

Other PDB entries of the same protein (UniProt Q9UBL3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F6L 1.9 Å, The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L
3TOJ 2.07 Å, Structure of the SPRY domain of human Ash2L
3RSN 2.1 Å, Crystal Structure of the N-terminal region of Human Ash2L
4X8N 2.1 Å, Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5
7W67 2.19 Å, The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with…
4X8P 2.2 Å, Crystal structure of Ash2L SPRY domain in complex with RbBP5
7W6A 2.21 Å, Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex
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…
5F6K 2.41 Å, Crystal structure of the MLL3-Ash2L-RbBP5 complex
3S32 2.45 Å, Crystal structure of Ash2L N-terminal domain
7W6I 2.56 Å, The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with…

Browse structure collections

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