6PWX: RbBP5

Cryo-EM structure of RbBP5 bound to the nucleosome. Determined by electron microscopy at 4.2 Å resolution. Released 18 Dec 2019.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Homo sapiens, Xenopus laevis, synthetic construct
Chains: 11
Atoms: 14,411
Mol. weight: 258.86 kDa
Released: 18 Dec 2019

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

Secondary structure: helices and β-sheets

6PWX contains 40 α-helices and 50 β-strands across 9 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	1
β-strand	27	1	2
β-strand	31-32	2	3
β-strand	38-42	5	3
β-strand	43	1	2
β-strand	48-52	5	3
β-strand	57-62	6	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	110-115	6	5
β-strand	122-127	6	5
β-strand	133-136	4	5
β-strand	142-144	3	5
β-strand	156-159	4	6
β-strand	165-169	5	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
β-strand	243-245	3	7
α-helix	252-253	2
β-strand	254-259	6	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	309-314	6	1
β-strand	317-322	6	1

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	64-75	12
β-strand	83-84	2	9
α-helix	86-113	28
β-strand	118-119	2	10
α-helix	121-131	11

Chains H and L: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	10
α-helix	50-76	27
β-strand	80-81	2	9
α-helix	83-92	10
β-strand	97	1	11

Chain I: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	12
α-helix	46-72	27
β-strand	77-78	2	13
α-helix	80-89	10
α-helix	91-96	6
β-strand	101	1	14

Chain J: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	13
α-helix	53-80	28
β-strand	85-86	2	12
α-helix	88-98	11
α-helix	101-119	19

Chain M: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	17
α-helix	46-72	27
β-strand	77-78	2	18
α-helix	79	1
α-helix	80-88	9
α-helix	91-96	6
β-strand	101	1	11

Chain N: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	18
α-helix	53-80	28
β-strand	85-86	2	17
α-helix	88-98	11
α-helix	102-120	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-binding protein 5	A	protein	538	Homo sapiens	Q15291 (AlphaFold model)
Histone H3.2	G, K	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	H, L	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	I, M	protein	129	Xenopus laevis	P06897 (AlphaFold model)
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

>6PWX_1 Retinoblastoma-binding protein 5 (chains A)
SNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL

Sequence of entity 2 (G, K), FASTA

>6PWX_2 Histone H3.2 (chains G, K)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (H, L), FASTA

>6PWX_3 Histone H4 (chains H, L)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (I, M), FASTA

>6PWX_4 Histone H2A type 1 (chains I, M)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 5 (J, N), FASTA

>6PWX_5 Histone H2B 1.1 (chains J, N)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 6 (O), FASTA

>6PWX_6 DNA (146-MER) (chains O)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (P), FASTA

>6PWX_7 DNA (146-MER) (chains P)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

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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