8G87: Human Oct4

Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region). Determined by electron microscopy at 8.1 Å resolution. Released 22 Mar 2023.

Method: Electron microscopy
Resolution: 8.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,777
Mol. weight: 157.12 kDa
Released: 22 Mar 2023

Explore 8G87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G87 contains 8 α-helices and 0 β-strands across 1 chain. 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 X: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	142-160	19
α-helix	164-175	12
α-helix	181-188	8
α-helix	194-210	17
α-helix	216-219	4
α-helix	239-248	10
α-helix	257-267	11
α-helix	271-287	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
nMatn1 DNA (top strand)	I	DNA	186	Homo sapiens
nMatn1 DNA (bottom strand)	J	DNA	186	Homo sapiens
POU domain, class 5, transcription factor 1	X	protein	395	Homo sapiens	Q01860 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>8G87_1 nMatn1 DNA (top strand) (chains I)
ACATGCACACATGCTAATATATGCACACAATGCACACAGGTTAATATATACACATACACA
CACATGCACACACACGTGCACACATATATGCACATGCATGCACACACGTATATGCACACA
CATGCACATGCATGCGCACATAGTCACACACATGCACACATTAGCATATGCATACACATA
CATGCA

Sequence of entity 2 (J), FASTA

>8G87_2 nMatn1 DNA (bottom strand) (chains J)
TGCATGTATGTGTATGCATATGCTAATGTGTGCATGTGTGTGACTATGTGCGCATGCATG
TGCATGTGTGTGCATATACGTGTGTGCATGCATGTGCATATATGTGTGCACGTGTGTGTG
CATGTGTGTGTATGTGTATATATTAACCTGTGTGCATTGTGTGCATATATTAGCATGTGT
GCATGT

Sequence of entity 3 (X), FASTA

>8G87_3 POU domain, class 5, transcription factor 1 (chains X)
GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRDPNSMAGHLASDFAFSPPPGGGGDGPGGP
EPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLV
PQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKE
LEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQ
KWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQ
QLGLEKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGY
GSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN

Primary citation

Histone modifications regulate pioneer transcription factor cooperativity. Sinha, K.K., Bilokapic, S., Du, Y. et al. Nature (2023) 619:378-384. DOI 10.1038/s41586-023-06112-6 · PubMed

Other PDB entries of the same protein (UniProt Q01860 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G88 2.3 Å, Human Oct4 bound to nucleosome with human nMatn1 sequence
7U0G 2.6 Å, structure of LIN28b nucleosome bound 3 OCT4
7U0I 2.6 Å, Structure of LIN28b nucleosome bound 2 OCT4
8SPU 2.8 Å, Structure of ESRRB nucleosome bound OCT4 at site c
8SPS 3.0 Å, High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b
6T90 3.05 Å, OCT4-SOX2-bound nucleosome - SHL-6
8G8G 3.2 Å, Interaction of H3 tail in LIN28B nucleosome with Oct4
8OTS 3.3 Å, OCT4 and MYC-MAX co-bound to a nucleosome
6YOV 3.42 Å, OCT4-SOX2-bound nucleosome - SHL+6
9RL4 3.5 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
8G8E 3.9 Å, Human Oct4 bound to nucleosome with human LIN28B sequence
9RN2 4.1 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2

Browse structure collections

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