PDBsum entry 6t7b

Nuclear protein

PDB id: 6t7b

Contents

Protein chains

98 a.a.

84 a.a.

106 a.a.

95 a.a.

76 a.a.

DNA/RNA

PDB id:

6t7b

Name:

Nuclear protein

Title:

Structure of human sox2 transcription factor in complex with a nucleosome

Structure:

Histone h3.2. Chain: a, e. Synonym: histone h3/m,histone h3/o. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a type 1-b/e. Chain: c, g.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hist2h3a, hist2h3c, h3f2, h3fm, hist2h3d. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hist1h4a, h4/a, h4fa, hist1h4b, h4/i, h4fi, hist1h4c, h4/g, h4fg, hist1h4d, h4/b, h4fb, hist1h4e, h4/j, h4fj, hist1h4f, h4/c, h4fc, hist1h4h, h4/h, h4fh, hist1h4i, h4/m, h4fm, hist1h4j, h4/e,

Authors:

S.O.Dodonova,F.Zhu,C.Dienemann,J.Taipale,P.Cramer

Key ref:

S.O.Dodonova et al. (2020). Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature, 580, 669-672. PubMed id: 32350470 DOI: 10.1038/s41586-020-2195-y

Date:

21-Oct-19 Release date: 29-Apr-20

Protein chains

Q71DI3  (H32_HUMAN) -  Histone H3.2 from Homo sapiens

Seq: 136 a.a.

Struc: 98 a.a.*

Protein chains

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 84 a.a.

Protein chains

P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E from Homo sapiens

Seq: 130 a.a.

Struc: 106 a.a.

Protein chains

O60814  (H2B1K_HUMAN) -  Histone H2B type 1-K from Homo sapiens

Seq: 126 a.a.

Struc: 95 a.a.

Protein chain

P48431  (SOX2_HUMAN) -  Transcription factor SOX-2 from Homo sapiens

Seq: 317 a.a.

Struc: 76 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-T-A-A-T-T-T-A-T-G-T-T-T-G-T-T-A-G-C-G-T-T-A-T-A-C-T-A-T-T-C-T-A-A-T-T-C-T-T- 95 bases

C-G-T-T-A-G-G-C-A-T-T-A-A-G-C-T-G-A-A-C-G-C-A-C-A-A-A-G-G-A-A-C-A-A-A-A-T-A-A- 95 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, K: E.C.?

DOI no: 10.1038/s41586-020-2195-y

Nature 580:669-672 (2020)

PubMed id: 32350470

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.

S.O.Dodonova, F.Zhu, C.Dienemann, J.Taipale, P.Cramer.

ABSTRACT

'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming^1,2. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells³. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.