9QPF: Sox2 DBD

Solution structure of Sox2 DBD. Determined by solution NMR. Released 19 Nov 2025.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 822
Mol. weight: 11.77 kDa
Released: 19 Nov 2025

Explore 9QPF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QPF contains 3 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 A: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	47-62	16
α-helix	68-81	14
α-helix	84-103	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor SOX-2	A	protein	97	Homo sapiens	P48431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9QPF_1 Transcription factor SOX-2 (chains A)
GSNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPF
IDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTL

Primary citation

Solution structure of the Sox2 DNA-binding domain reveals conformational selection in DNA binding. Orsetti, A., Slejfer, J., Ha, S. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf1121 · PubMed

Other PDB entries of the same protein (UniProt P48431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WX8 2.3 Å, SOX2 bound to Importin-alpha 3
6WX7 2.7 Å, SOX2 bound to Importin-alpha 2
6WX9 2.8 Å, SOX2 bound to Importin-alpha 5
6T90 3.05 Å, OCT4-SOX2-bound nucleosome - SHL-6
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
9RN2 4.1 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2
9RMC 4.2 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1
6T7B 5.1 Å, Structure of human Sox2 transcription factor in complex with a nucleosome
9RN1 5.9 Å, Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47…
1O4X Ternary complex of the DNA binding domains of the OCT1 and SOX2 transcription factors…
2LE4 Solution structure of the HMG box DNA-binding domain of human stem cell transcription…

Browse structure collections

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