8A40

Structure of mammalian Pol II-TFIIS elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of a backtracked hexasomal intermediate of nucleosome transcription.

Farnung, L.Ochmann, M.Garg, G.Vos, S.M.Cramer, P.

(2022) Mol Cell 82: 3126-3134.e7

  • DOI: https://doi.org/10.1016/j.molcel.2022.06.027
  • Primary Citation of Related Structures:  
    8A40

  • PubMed Abstract: 

    During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS are present. The cryo-EM structure of an intermediate of the nucleosome passage shows a partially unraveled hexasome that lacks the proximal H2A-H2B dimer and interacts with the RNA Pol II jaw, DSIF, and the CTR9trestle helix. RNA Pol II adopts a backtracked state with the RNA 3' end dislodged from the active site and bound in the RNA Pol II pore. Additional structures and biochemical data show that human TFIIS enters the RNA Pol II pore and stimulates the cleavage of the backtracked RNA and nucleosome passage.


  • Organizational Affiliation

    Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: lucas_farnung@hms.harvard.edu.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,984Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A7M4DUC2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,251Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a117Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1P [auth U]304Homo sapiensMutation(s): 0 
Gene Names: TCEA1
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PHAROS:  P23193
GTEx:  ENSG00000187735 
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Entity ID: 13
MoleculeChains LengthOrganismImage
Non-template DNAM [auth N]48synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNAN [auth P]14synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
Template DNAO [auth T]41synthetic 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 
AA [auth I]
BA [auth I]
CA [auth I]
DA [auth U]
Q [auth A]
AA [auth I],
BA [auth I],
CA [auth I],
DA [auth U],
Q [auth A],
R [auth A],
T [auth A],
U [auth A],
W [auth A],
Y [auth B],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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)GermanySFB860
German Research Foundation (DFG)GermanyEXC 2067/1-390729940

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release