7NKY

RNA Polymerase II-Spt4/5-nucleosome-FACT structure


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of nucleosome transcription mediated by Chd1 and FACT.

Farnung, L.Ochmann, M.Engeholm, M.Cramer, P.

(2021) Nat Struct Mol Biol 28: 382-387

  • DOI: https://doi.org/10.1038/s41594-021-00578-6
  • Primary Citation of Related Structures:  
    7NKX, 7NKY

  • PubMed Abstract: 

    Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA.


  • Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1D [auth A]1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2E [auth B]1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3F [auth C]318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1G [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2H [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3I [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9J [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5K [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11L [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4M [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin elongation factor SPT4N [auth Y]102Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2707PACBIOSEQ_LOCUS2757SCNYR20_0003027800SCP684_0002027900
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5O [auth Z]1,064Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4816
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4P [auth D]221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7Q [auth G]171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit POB3R [auth O]552Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4754SCNYR20_0006005900SCP684_0006005800
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit SPT16S [auth Q]1,035Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT16CDC68SSF1YGL207W
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2T [auth a],
X [auth e]
136Xenopus laevisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4U [auth b],
Y [auth f]
103Xenopus laevisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1V [auth c],
Z [auth g]
130Xenopus laevisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1AA [auth h],
W [auth d]
123Xenopus laevisMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3')A [auth P]16synthetic RNA
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (138-MER)B [auth N]138synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (148-MER)C [auth T]148synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
EA [auth B]
FA [auth C]
GA [auth I]
BA [auth A],
CA [auth A],
EA [auth B],
FA [auth C],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth L],
KA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union693023
German Research Foundation (DFG)GermanyEXC 2067/1- 390729940
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySPP2191

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references