8OTT: MYC-MAX

Name: PDB 8OTT: MYC-MAX bound to a nucleosome at SHL+5.8
Published: 2023-05-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

MYC-MAX bound to a nucleosome at SHL+5.8. Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 12
Atoms: 12,973
Mol. weight: 187.37 kDa
Ligands: PTD
Released: 24 May 2023

Explore 8OTT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OTT contains 46 α-helices and 20 β-strands across 10 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, 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	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	97-98	2	3

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	6
α-helix	113-115	3

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	104-122	19

Chain E: 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	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
α-helix	36-38	3
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	3

Chain M: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	354-379	26
α-helix	382-384	3
α-helix	392-404	13

1 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
Histone H3.1	A, E	protein	95	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	82	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C	protein	109	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	93	Homo sapiens	P06899 (AlphaFold model)
Histone H2A type 1-K	G	protein	108	Homo sapiens	Q8CGP7
DNA (144-mer)	I	DNA	144	synthetic construct
DNA (144-mer)	J	DNA	144	synthetic construct
Myc proto-oncogene protein	M	protein	53	Homo sapiens	P01106
Protein max	N	protein	51	Homo sapiens	P61244

Sequence of entity 1 (A, E), FASTA

>8OTT_1 Histone H3.1 (chains A, E)
HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEA
YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE

Sequence of entity 2 (B, F), FASTA

>8OTT_2 Histone H4 (chains B, F)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C), FASTA

>8OTT_3 Histone H2A type 1-B/E (chains C)
GKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAG
NAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL

Sequence of entity 4 (D, H), FASTA

>8OTT_4 Histone H2B type 1-J (chains D, H)
SRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Sequence of entity 5 (G), FASTA

>8OTT_5 Histone H2A type 1-K (chains G)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP

Sequence of entity 6 (I), FASTA

>8OTT_6 DNA (144-MER) (chains I)
GGAGAATCCCGGTCTGCAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAAC
GCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGG
CACGGGTCACGTGCATACATCCTG

Sequence of entity 7 (J), FASTA

>8OTT_7 DNA (144-MER) (chains J)
CAGGATGTATGCACGTGACCCGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTGCAGACCGGGATTCTCC

Sequence of entity 8 (M), FASTA

>8OTT_8 Myc proto-oncogene protein (chains M)
NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILS

Sequence of entity 9 (N), FASTA

>8OTT_9 Protein max (chains N)
DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQY

Ligands and cofactors

ID	Name	Formula	Copies
PTD	Pentanedial	C5 H8 O2	8

Primary citation

Cooperation between bHLH transcription factors and histones for DNA access. Michael, A.K., Stoos, L., Crosby, P. et al. Nature (2023) 619:385-393. DOI 10.1038/s41586-023-06282-3 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

Browse structure collections

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