SMTL ID : 6yov.1

OCT4-SOX2-bound nucleosome - SHL+6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-1-1-1-1-mer

Ligands

8 x PTD: PENTANEDIAL(Covalent)

PTD.1: 2 residues within 4Å: Chain A: K.119 Chain E: K.126 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:K.119, E:K.126 PTD.2: 2 residues within 4Å: Chain A: K.126 Chain E: K.119 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:K.119, A:K.126 PTD.3: 2 residues within 4Å: Chain A: K.83 Chain B: K.82 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.83, B:K.82 PTD.4: 3 residues within 4Å: Chain C: K.40 Chain H: H.86, K.89 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:K.89, C:K.40 PTD.5: 2 residues within 4Å: Chain D: K.47, K.50 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.47, D:K.50 PTD.6: 2 residues within 4Å: Chain D: K.89 Chain G: K.40 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:K.89, G:K.40 PTD.7: 2 residues within 4Å: Chain E: K.83 Chain F: K.83 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:K.83, F:K.83 PTD.8: 2 residues within 4Å: Chain H: K.47, K.50 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:K.47, H:K.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michael, A.K. et al., Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science (2020)

Release Date

2020-05-06

Peptides

Histone H3.1: A
Histone H4: B
Histone H2A type 1-B/E: CG
Histone H2B type 1-J: DH
Histone H3.1: E
Histone H4: F
Green fluorescent protein,POU domain, class 5, transcription factor 1: K
Transcription factor SOX-2: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

G
G

D
D

H
H

E
E

F
F

K
K

L
L

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

Histone H3.1

Histone H4

Green fluorescent protein,POU domain, class 5, transcription factor 1

Transcription factor SOX-2

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