6PWV: MLL1 core complex

Cryo-EM structure of MLL1 core complex bound to the nucleosome. Determined by electron microscopy at 6.2 Å resolution. Released 18 Dec 2019.

Method: Electron microscopy
Resolution: 6.2 Å
Organisms: Homo sapiens, Xenopus laevis, synthetic construct
Chains: 16
Atoms: 21,781
Mol. weight: 401.26 kDa
Ligands: ZN, SAH
Released: 18 Dec 2019

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

Secondary structure: helices and β-sheets

6PWV contains 61 α-helices and 111 β-strands across 14 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, 32 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	1
β-strand	27	1	2
β-strand	29-32	4	3
β-strand	38-42	5	3
β-strand	47-52	6	3
β-strand	57-63	7	3
α-helix	68	1
β-strand	69-74	6	4
β-strand	80-85	6	4
β-strand	89-94	6	4
β-strand	100-105	6	4
β-strand	110-116	7	5
β-strand	119-127	9	5
α-helix	131-132	2
β-strand	133-136	4	5
β-strand	142-144	3	5
α-helix	145-146	2
β-strand	155-159	5	6
β-strand	165-170	6	6
β-strand	174-179	6	6
β-strand	185-190	6	6
β-strand	201-206	6	7
β-strand	212-217	6	7
β-strand	222-226	5	7
α-helix	227-233	7
α-helix	239-241	3
β-strand	243-245	3	7
β-strand	256-259	4	8
β-strand	265-270	6	8
β-strand	275-280	6	8
β-strand	286-291	6	8
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	9
β-strand	343-344	2	9

Chain B: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	10
β-strand	48-53	6	11
β-strand	59-64	6	11
β-strand	68-73	6	11
β-strand	79-84	6	11
β-strand	90-95	6	12
β-strand	101-106	6	12
β-strand	110-115	6	12
β-strand	121-126	6	12
β-strand	132-137	6	13
β-strand	143-148	6	13
β-strand	153-157	5	13
β-strand	163-167	5	13
β-strand	174-179	6	14
β-strand	185-190	6	14
β-strand	195-199	5	14
β-strand	205-209	5	14
β-strand	217-222	6	15
β-strand	228-233	6	15
β-strand	237-242	6	15
β-strand	248-252	5	15
β-strand	264-267	4	16
β-strand	273-277	5	16
β-strand	283-287	5	16
β-strand	293-297	5	16
β-strand	304-309	6	10
β-strand	315-320	6	10
β-strand	326-331	6	10

Chain C: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3816-3830	15
β-strand	3831-3835	5	17
β-strand	3841-3845	5	17
α-helix	3848	1
β-strand	3849	1	18
α-helix	3850	1
β-strand	3854-3857	4	19
β-strand	3860-3864	5	9
α-helix	3865-3867	3
α-helix	3868-3878	11
β-strand	3884-3886	3	9
β-strand	3891-3899	9	9
α-helix	3901-3904	4
β-strand	3906-3907	2	20
β-strand	3913-3920	8	19
β-strand	3923-3930	8	19
β-strand	3934	1	18
α-helix	3938	1
β-strand	3939	1	17
α-helix	3940	1
β-strand	3941-3942	2	20
β-strand	3956	1	21
β-strand	3967	1	21

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	194-196	3
α-helix	227-230	4
β-strand	235	1	30
β-strand	247-251	5	31
α-helix	291-293	3
β-strand	298-301	4	30
β-strand	306-309	4	30
β-strand	314-317	4	32
β-strand	322	1	33
β-strand	325-335	11	30
β-strand	343-347	5	32
β-strand	363-368	6	32
β-strand	371-375	5	32
β-strand	378-380	3	32
β-strand	391-398	8	30
α-helix	401-405	5
α-helix	412-414	3
β-strand	416-420	5	31
β-strand	423-429	7	31
α-helix	441-442	2
β-strand	446-451	6	30
β-strand	454-460	7	30
β-strand	468	1	33
β-strand	469-474	6	32
β-strand	479-483	5	30
β-strand	498	1	30
α-helix	500-523	24

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	53-60	8
α-helix	62-75	14
α-helix	80-90	11

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	53-75	23
α-helix	80-90	11

Chain G: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	22
α-helix	86-113	28
α-helix	121-130	10

Chain H: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
α-helix	50-76	27
β-strand	80-81	2	22
α-helix	83-92	10
β-strand	97	1	23

6 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	122	Xenopus laevis	P02281
DNA (147-mer)	O	DNA	147	synthetic construct
DNA (147-mer)	P	DNA	147	synthetic construct
Protein dpy-30 homolog	E, F	protein	102	Homo sapiens	Q9C005
Set1/Ash2 histone methyltransferase complex subunit ASH2	D	protein	534	Homo sapiens	Q9UBL3

Sequence of entity 1 (A), FASTA

>6PWV_1 Retinoblastoma-binding protein 5 (chains A)
SNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL

Sequence of entity 2 (B), FASTA

>6PWV_2 WD repeat-containing protein 5 (chains B)
SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEK
TISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQS
NLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTA
SGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYC
IFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAAL
ENDKTIKLWKSDC

Sequence of entity 3 (C), FASTA

>6PWV_3 Histone-lysine N-methyltransferase 2A (chains C)
SGSARAEVHLRKSAFDMFNFLASKHRQPPEYNPNDEEEEEVQLKSARRATSMDLPMPMRF
RHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGIVIRSILTDKREKYYDSKGI
GCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEEL
TYDYKFPIEDASNKLPCNCGAKKCRKFLN

Sequence of entity 4 (G, K), FASTA

>6PWV_4 Histone H3.2 (chains G, K)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 5 (H, L), FASTA

>6PWV_5 Histone H4 (chains H, L)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (I, M), FASTA

>6PWV_6 Histone H2A type 1 (chains I, M)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 7 (J, N), FASTA

>6PWV_7 Histone H2B 1.1 (chains J, N)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 8 (O), FASTA

>6PWV_8 DNA (147-MER) (chains O)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 9 (P), FASTA

>6PWV_9 DNA (147-MER) (chains P)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 10 (E, F), FASTA

>6PWV_10 Protein dpy-30 homolog (chains E, F)
SGSMEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRAYL
DQTVVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN

Sequence of entity 11 (D), FASTA

>6PWV_11 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains D)
SDTQAGSVDEENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSG
NTYFLRKQANLKEMCLSALANLTWQSRTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRP
GKMTWPNNIVKTMSKERDVFLVKEHPDPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQS
SAVSTSGNLNGGIAAGSSGKGRGAKRKQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEH
PFNKDGYRYILAEPDPHAPDPEKLELDCWAGKPIPGDLYRACLYERVLLALHDRAPQLKI
SDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYD
KFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTETAKSLPDTYKDKALIKF
KSYLYFEEKDFVDKAEKSLKQTPHSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTV
SINFGPCFKYPPKDLTYRPMSDMGWGAVVEHTLADVLYHVETEVDGRRSPPWEP

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

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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