8A3Y

Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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:  
    8A3Y, 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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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,251Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3270Sus scrofaMutation(s): 0 
Gene Names: POLR2C
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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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 polymerase II subunit E210Sus 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 
UniProt
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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
Find proteins for A0A8D0JYF1 (Sus scrofa)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SPT61,002Homo sapiensMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1P [auth Q],
S [auth U]
1,845Homo sapiensMutation(s): 0 
Gene Names: CTR9KIAA0155SH2BP1LEO1RDL
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GTEx:  ENSG00000198730 
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GTEx:  ENSG00000166477 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1 homologQ [auth R]248Homo sapiensMutation(s): 0 
Gene Names: RTF1KIAA0252
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GTEx:  ENSG00000137815 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated factor 1 homologT [auth V]311Homo sapiensMutation(s): 0 
Gene Names: PAF1PD2
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GTEx:  ENSG00000006712 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 61U [auth W]305Homo sapiensMutation(s): 0 
Gene Names: WDR61
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GTEx:  ENSG00000140395 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ParafibrominV [auth X]531Homo sapiensMutation(s): 0 
Gene Names: CDC73C1orf28HRPT2
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GTEx:  ENSG00000134371 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4W [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1QtsA-10763
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5X [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2CA [auth e],
Y [auth a]
136Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4DA [auth f],
Z [auth b]
103Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AAA [auth c]103Xenopus laevisMutation(s): 0 
Gene Names: LOC494591h2ac14.Lhist1h2ajhist1h2aj.LXELAEV_18003602mg
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BBA [auth d]95Xenopus laevisMutation(s): 0 
Gene Names: LOC108704302
UniProt
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA127synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA, Template DNAO [auth P]28synthetic construct
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Entity ID: 18
MoleculeChains LengthOrganismImage
RNA, Template DNAR [auth T]138synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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EA [auth A]
FA [auth A]
GA [auth B]
HA [auth C]
IA [auth I]
EA [auth A],
FA [auth A],
GA [auth B],
HA [auth C],
IA [auth I],
JA [auth I],
KA [auth J],
LA [auth L],
NA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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MA [auth P]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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: 2024-07-31
    Type: Initial release