6T7B: Human Sox2 transcription factor

Structure of human Sox2 transcription factor in complex with a nucleosome. Determined by electron microscopy at 5.1 Å resolution. Released 29 Apr 2020.

Method: Electron microscopy
Resolution: 5.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 7,248
Mol. weight: 216.33 kDa
Released: 29 Apr 2020

Explore 6T7B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T7B contains 41 α-helices and 16 β-strands across 9 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-74	11
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
α-helix	80-88	9
β-strand	101-102	2	5

Chain D: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	35-45	11
α-helix	54-80	27
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-120	19

Chain E: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	45-56	12
α-helix	64-74	11
β-strand	83-84	2	6
α-helix	86-113	28
α-helix	121-130	10

Chain F: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
α-helix	32-40	9
α-helix	48-50	3
α-helix	51-75	25
β-strand	80-81	2	6
α-helix	83-91	9
α-helix	96	1
β-strand	97-98	2	5

Chain G: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	7
α-helix	46-72	27
β-strand	77-78	2	8
α-helix	80-88	9
β-strand	101-102	2	3

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	35-45	11
β-strand	50-51	2	8
α-helix	54-80	27
β-strand	85-86	2	7
α-helix	88-98	11
α-helix	102-120	19

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 H3.2	A, E	protein	136	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	151	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	126	Homo sapiens	O60814 (AlphaFold model)
DNA (147-mer)	I	DNA	147	synthetic construct
DNA (147-mer)	J	DNA	147	synthetic construct
Transcription factor SOX-2	K	protein	89	Homo sapiens	P48431

Sequence of entity 1 (A, E), FASTA

>6T7B_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6T7B_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6T7B_3 Histone H2A type 1-B/E (chains C, G)
MGSSHHHHHHENLYFQSNAPWMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGN
YSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLG
RVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>6T7B_4 Histone H2B type 1-K (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>6T7B_5 DNA (147-MER) (chains I)
ATCTACACGACGCTCTTCCGATCTAATTTATGTTTGTTAGCGTTATACTATTCTAATTCT
TTGTTTCGGTGGTATTGTTTATTTTGTTCCTTTGTGCGTTCAGCTTAATGCCTAACGACA
CTCGGAGATCGGAAGAGCACACGTGAT

Sequence of entity 6 (J), FASTA

>6T7B_6 DNA (147-MER) (chains J)
ATCACGTGTGCTCTTCCGATCTCCGAGTGTCGTTAGGCATTAAGCTGAACGCACAAAGGA
ACAAAATAAACAATACCACCGAAACAAAGAATTAGAATAGTATAACGCTAACAAACATAA
ATTAGATCGGAAGAGCGTCGTGTAGAT

Sequence of entity 7 (K), FASTA

>6T7B_7 Transcription factor SOX-2 (chains K)
SNANSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFID
EAKRLRALHMKEHPDYKYRPRRKTKTLMK

Primary citation

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Dodonova, S.O., Zhu, F., Dienemann, C. et al. Nature (2020) 580:669-672. DOI 10.1038/s41586-020-2195-y · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

Browse structure collections

About this viewer

MolViewer shows 6T7B directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.