6T79

Structure of a human nucleosome at 3.2 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb6T79/pdb
• NAKB: 6T79
• EM Map EMD-10390: EMDB EMDataResource

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-21 Released: 2020-04-29 
• Deposition Author(s): Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P.
• Funding Organization(s): European Research Council, European Molecular Biology Organization, Volkswagen Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

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

(2020) Nature 580: 669-672

• PubMed: 32350470 
• DOI: https://doi.org/10.1038/s41586-020-2195-y
• Primary Citation of Related Structures:  
  6T78, 6T79, 6T7A, 6T7B, 6T7C, 6T7D


• PubMed 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 cells ³ . 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.

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Organizational Affiliation: 

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer - A6B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 205.55 kDa 
• Atom Count: 12,121 
• Modelled Residue Count: 1,066 
• Deposited Residue Count: 1,326 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Homo sapiens	Mutation(s): 1  Gene Names: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D, H3C15, H3C14, H3C13
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Homo sapiens	Mutation(s): 0  Gene Names:  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, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	151	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BK, H2BFT, HIRIP1, H2BC12
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	I	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	J	147	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P.

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Funding Organization	Location	Grant Number
European Research Council	Germany	693023
European Molecular Biology Organization	Germany	ALTF-949-2016
Volkswagen Foundation	Germany	--

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references