5F6K: MLL3-Ash2L-RbBP5 complex
Crystal structure of the MLL3-Ash2L-RbBP5 complex. Determined by X-ray diffraction at 2.41 Å resolution. Released 24 Feb 2016.
- Method
- X-ray diffraction
- Resolution
- 2.41 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 5,829
- Mol. weight
- 86.55 kDa
- Ligands
- SAH, ZN
- Released
- 24 Feb 2016
Explore 5F6K in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5F6K contains 18 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.
Chains A and B: 2 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 |
| β-strand | 373-375 | 3 | 1 |
| β-strand | 378-380 | 3 | 1 |
| β-strand | 391-398 | 8 | 2 |
| β-strand | 446-451 | 6 | 2 |
| β-strand | 454-461 | 8 | 2 |
| α-helix | 463-464 | 2 | |
| 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 C: 7 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4758-4768 | 11 | |
| 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 | 4807-4817 | 11 | |
| 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 |
| 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: 7 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4758-4765 | 8 | |
| α-helix | 4769-4771 | 3 | |
| β-strand | 4773-4777 | 5 | 13 |
| β-strand | 4783-4787 | 5 | 13 |
| β-strand | 4791 | 1 | 14 |
| β-strand | 4796-4799 | 4 | 15 |
| β-strand | 4803-4806 | 4 | 16 |
| α-helix | 4807-4819 | 13 | |
| 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 | 15 |
| β-strand | 4855-4862 | 8 | 15 |
| β-strand | 4865-4872 | 8 | 15 |
| β-strand | 4876 | 1 | 14 |
| α-helix | 4880 | 1 | |
| β-strand | 4881 | 1 | 13 |
| α-helix | 4882 | 1 | |
| β-strand | 4883-4884 | 2 | 15 |
| β-strand | 4897-4898 | 2 | 17 |
| β-strand | 4909-4910 | 2 | 17 |
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,Set1/Ash2 histone methyltransferase… | 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) |
| peptide ARTKQTARK | M | protein | 9 | Homo sapiens | Q6NXT2 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>5F6K_1 Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains A, B)
SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARL
GWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTIS
GRGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPM
SDMG
Sequence of entity 2 (C, E), FASTA
>5F6K_2 Histone-lysine N-methyltransferase 2C (chains C, E)
GPLGSKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANR
KEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVVTFERGHKIIISS
SRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN
Sequence of entity 3 (D, F), FASTA
>5F6K_3 Retinoblastoma-binding protein 5 (chains D, F)
SAFAPDFKELDENVEYEERESEFDIED
Sequence of entity 4 (M), FASTA
>5F6K_4 peptide ARTKQTARK (chains M)
ARTKQTARK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 2 |
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structural basis for activity regulation of MLL family methyltransferases. Li, Y., Han, J., Zhang, Y. et al. Nature (2016) 530:447-452. DOI 10.1038/nature16952 · 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…
- 7W6L 2.26 Å, The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide
- 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
About this viewer
MolViewer shows 5F6K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.