8DK5: 187bp LIN28b nucleosome with site 0 mutation

Structure of 187bp LIN28b nucleosome with site 0 mutation. Determined by electron microscopy at 2.71 Å resolution. Released 28 Jun 2023.

Method: Electron microscopy
Resolution: 2.71 Å
Organisms: Homo sapiens, Mus musculus
Chains: 12
Atoms: 15,618
Mol. weight: 283.1 kDa
Released: 28 Jun 2023

Explore 8DK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DK5 contains 45 α-helices and 74 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	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-71	25
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	5
α-helix	57-84	28
β-strand	89-90	2	4
α-helix	92-102	11
α-helix	105-122	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
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	26-28	3
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	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
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	100-102	3	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	10
α-helix	57-84	28
β-strand	89-90	2	9
α-helix	92-102	11
α-helix	105-124	20

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
Histone H3.1	A, E	protein	136	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 2-C	C, G	protein	129	Homo sapiens	Q16777 (AlphaFold model)
Histone H2B type 2-E	D, H	protein	126	Homo sapiens	Q16778 (AlphaFold model)
Single-chain variable fragment	K, N	protein	265	Mus musculus
DNA (187-mer)	I	DNA	187	Homo sapiens
DNA (187-mer)	J	DNA	187	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>8DK5_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8DK5_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8DK5_3 Histone H2A type 2-C (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHKAKSK

Sequence of entity 4 (D, H), FASTA

>8DK5_4 Histone H2B type 2-E (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 5 (K, N), FASTA

>8DK5_5 Single-chain variable fragment (chains K, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA

Sequence of entity 6 (I), FASTA

>8DK5_6 DNA (187-MER) (chains I)
GCATAAGTTAAGTGGAGAGAAAGAATCCTCAGTGGTGAGTATTAACATGGAACTTACTCC
AACAATACAGATGCTGAATAAATGTAGTCTAAGTGAAGGAAGAAGGAAAGGTGGGAGCTG
CCATCACTCAGAATTGTCCAGCAGGGATTGTGCAAGCTTGTGAATAAAGACACATACTTC
ATGTAGT

Sequence of entity 7 (J), FASTA

>8DK5_7 DNA (187-MER) (chains J)
ACTACATGAAGTATGTGTCTTTATTCACAAGCTTGCACAATCCCTGCTGGACAATTCTGA
GTGATGGCAGCTCCCACCTTTCCTTCTTCCTTCACTTAGACTACATTTATTCAGCATCTG
TATTGTTGGAGTAAGTTCCATGTTAATACTCACCACTGAGGATTCTTTCTCTCCACTTAA
CTTATGC

Primary citation

Structural mechanism of LIN28B nucleosome targeting by OCT4. Guan, R., Lian, T., Zhou, B.R. et al. Mol Cell (2023) 83:1970-1982.e6. DOI 10.1016/j.molcel.2023.05.030 · 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

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