6KM7: The internal interaction in RBBP5

The structural basis for the internal interaction in RBBP5. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Oct 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,963
Mol. weight: 87.01 kDa
Ligands: 2PE
Released: 2 Oct 2019

Explore 6KM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KM7 contains 9 α-helices and 62 β-strands across 4 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: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	1
β-strand	27-32	6	2
β-strand	38-43	6	2
β-strand	47-52	6	2
β-strand	57-63	7	2
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
β-strand	133-136	4	4
β-strand	141-144	4	4
α-helix	145-146	2
β-strand	155-159	5	5
β-strand	165-170	6	5
β-strand	174-179	6	5
β-strand	185-190	6	5
β-strand	192	1	6
β-strand	198	1	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	254-259	6	8
β-strand	265-270	6	8
β-strand	275-280	6	8
β-strand	286-291	6	8
α-helix	296-297	2
β-strand	298-303	6	1
β-strand	310-314	5	1
β-strand	317-322	6	1

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	9
β-strand	27-32	6	10
β-strand	38-43	6	10
β-strand	47-52	6	10
β-strand	57-63	7	10
α-helix	68	1
β-strand	69-74	6	11
β-strand	80-85	6	11
β-strand	89-94	6	11
β-strand	100-105	6	11
β-strand	110-116	7	12
β-strand	119-127	9	12
β-strand	133-136	4	12
β-strand	141-144	4	12
α-helix	145-146	2
β-strand	155-159	5	13
β-strand	165-170	6	13
β-strand	174-179	6	13
β-strand	185-190	6	13
β-strand	192	1	14
β-strand	198	1	14
β-strand	201-206	6	15
β-strand	212-217	6	15
β-strand	222-226	5	15
α-helix	227-233	7
α-helix	239-241	3
β-strand	243-245	3	15
β-strand	254-259	6	16
β-strand	265-270	6	16
β-strand	275-280	6	16
β-strand	286-291	6	16
β-strand	298-303	6	9
β-strand	309-314	6	9
β-strand	317-322	6	9

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	453-456	4	3

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	449-453	5
β-strand	454-456	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-binding protein 5	A, B	protein	317	Homo sapiens	Q15291 (AlphaFold model)
Retinoblastoma-binding protein 5	C, D	protein	69	Homo sapiens	Q15291 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6KM7_1 Retinoblastoma-binding protein 5 (chains A, B)
SGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAKIISAHIHP
VCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQNKVLVCPM
KSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKTDSQDLVAS
FRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPEPMQKLQDL
VNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLDVAWHPVRP
IIASISSGVVSIWAQNQ

Sequence of entity 2 (C, D), FASTA

>6KM7_2 Retinoblastoma-binding protein 5 (chains C, D)
DEELEDSKALLYLPIAPEVEDPEENPYGPPPDGSQPPKKKPKTTNIELQGVPNDEVHPLL
GVKGDGKSK

Ligands and cofactors

ID	Name	Formula	Copies
2PE	Nonaethylene glycol	C18 H38 O10	1

Water and common crystallization additives (PG4, P6G, SO4) are not listed.

Primary citation

The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex. Han, J., Li, T., Li, Y. et al. Nucleic Acids Res (2019) 47:10426-10438. DOI 10.1093/nar/gkz819 · PubMed

Other PDB entries of the same protein (UniProt Q15291 (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
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
6KIU 3.2 Å, Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)

Browse structure collections

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