6PWW: MLL1

Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome. Determined by electron microscopy at 4.4 Å resolution. Released 18 Dec 2019.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Homo sapiens, Xenopus laevis, synthetic construct
Chains: 13
Atoms: 18,174
Mol. weight: 317.84 kDa
Ligands: ZN, SAH
Released: 18 Dec 2019

Explore 6PWW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PWW contains 46 α-helices and 92 β-strands across 11 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, 31 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	1
β-strand	27-32	6	2
β-strand	38-43	6	2
β-strand	47-52	6	2
β-strand	57-62	6	2
α-helix	68	1
β-strand	69-74	6	3
β-strand	80-85	6	3
β-strand	89-94	6	3
β-strand	100-105	6	3
β-strand	110-116	7	4
β-strand	119-127	9	4
α-helix	131-132	2
β-strand	133-136	4	4
β-strand	142-144	3	4
α-helix	145-146	2
β-strand	156-159	4	5
β-strand	165-169	5	5
β-strand	174-179	6	5
β-strand	184-190	7	5
β-strand	201-205	5	6
β-strand	212-217	6	6
β-strand	221-226	6	6
α-helix	227-233	7
α-helix	239-241	3
β-strand	243-246	4	6
β-strand	256-258	3	7
β-strand	265-270	6	7
β-strand	275-280	6	7
β-strand	286-291	6	7
β-strand	298-303	6	1
β-strand	310-314	5	1
β-strand	316	1	2
β-strand	317-321	5	1
β-strand	337-338	2	8
β-strand	343-344	2	8

Chain B: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	9
β-strand	48-53	6	10
β-strand	59-64	6	10
β-strand	69-73	5	10
β-strand	79-83	5	10
β-strand	90-95	6	11
β-strand	101-106	6	11
β-strand	110-115	6	11
β-strand	121-125	5	11
β-strand	132-137	6	12
β-strand	143-148	6	12
β-strand	153-157	5	12
β-strand	163-167	5	12
β-strand	174-179	6	13
β-strand	185-190	6	13
β-strand	195-199	5	13
β-strand	205-209	5	13
β-strand	217-222	6	14
β-strand	228-233	6	14
β-strand	237-242	6	14
β-strand	247-253	7	14
β-strand	264-267	4	15
β-strand	273-277	5	15
β-strand	282-287	6	15
β-strand	293-298	6	15
β-strand	306-309	4	9
β-strand	315-319	5	9
β-strand	326-331	6	9

Chain C: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3816-3826	11
β-strand	3831-3835	5	16
β-strand	3841-3845	5	16
β-strand	3849	1	17
β-strand	3854-3857	4	18
β-strand	3860-3864	5	8
α-helix	3865-3878	14
β-strand	3884-3886	3	8
β-strand	3891-3899	9	8
α-helix	3901-3904	4
α-helix	3905	1
β-strand	3906-3907	2	18
β-strand	3913-3920	8	18
β-strand	3923-3930	8	18
β-strand	3934	1	17
β-strand	3939	1	16
β-strand	3941-3942	2	18
α-helix	3946-3948	3

Chains G and K: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	19
α-helix	86-113	28
β-strand	118-119	2	20
α-helix	121-130	10

Chain H: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	20
α-helix	50-75	26
β-strand	80-81	2	19
α-helix	83-92	10
β-strand	97	1	21

Chain I: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	22
α-helix	46-72	27
β-strand	77-78	2	23
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	24

Chain J: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	23
α-helix	53-80	28
β-strand	85-86	2	22
α-helix	88-98	11
α-helix	102-119	18

Chain L: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	26
α-helix	50-75	26
β-strand	80-81	2	25
α-helix	83-92	10
β-strand	97-98	2	24

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-binding protein 5	A	protein	538	Homo sapiens	Q15291 (AlphaFold model)
WD repeat-containing protein 5	B	protein	313	Homo sapiens	P61964 (AlphaFold model)
Histone-lysine N-methyltransferase 2A	C	protein	209	Homo sapiens	Q03164
Histone H3.2	G, K	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	H, L	protein	103	Xenopus laevis	P62799
Histone H2A type 1	I, M	protein	129	Xenopus laevis	P06897
Histone H2B 1.1	J, N	protein	123	Xenopus laevis	P02281
DNA (146-mer)	O	DNA	147	synthetic construct
DNA (146-mer)	P	DNA	147	synthetic construct

Sequence of entity 1 (A), FASTA

>6PWW_1 Retinoblastoma-binding protein 5 (chains A)
SNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL

Sequence of entity 2 (B), FASTA

>6PWW_2 WD repeat-containing protein 5 (chains B)
SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEK
TISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQS
NLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTA
SGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYC
IFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAAL
ENDKTIKLWKSDC

Sequence of entity 3 (C), FASTA

>6PWW_3 Histone-lysine N-methyltransferase 2A (chains C)
SGSARAEVHLRKSAFDMFNFLASKHRQPPEYNPNDEEEEEVQLKSARRATSMDLPMPMRF
RHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGIVIRSILTDKREKYYDSKGI
GCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEEL
TYDYKFPIEDASNKLPCNCGAKKCRKFLN

Sequence of entity 4 (G, K), FASTA

>6PWW_4 Histone H3.2 (chains G, K)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 5 (H, L), FASTA

>6PWW_5 Histone H4 (chains H, L)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (I, M), FASTA

>6PWW_6 Histone H2A type 1 (chains I, M)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 7 (J, N), FASTA

>6PWW_7 Histone H2B 1.1 (chains J, N)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 8 (O), FASTA

>6PWW_8 DNA (146-MER) (chains O)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 9 (P), FASTA

>6PWW_9 DNA (146-MER) (chains P)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Primary citation

Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Park, S.H., Ayoub, A., Lee, Y.T. et al. Nat Commun (2019) 10:5540-5540. DOI 10.1038/s41467-019-13550-2 · PubMed

Other PDB entries of the same protein (UniProt Q15291 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KM7 1.8 Å, The structural basis for the internal interaction in RBBP5
5F6L 1.9 Å, The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and 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
7W6L 2.26 Å, The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide
3P4F 2.35 Å, Structural and biochemical insights into MLL1 core complex assembly and regulation.
5F6K 2.41 Å, Crystal structure of the MLL3-Ash2L-RbBP5 complex
7W6I 2.56 Å, The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with…
7W6J 2.68 Å, The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with…
7BRE 2.8 Å, The crystal structure of MLL2 in complex with ASH2L and RBBP5

Browse structure collections

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