6TED

Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.

Vos, S.M.Farnung, L.Linden, A.Urlaub, H.Cramer, P.

(2020) Nat Struct Mol Biol 27: 668-677

  • DOI: 10.1038/s41594-020-0437-1
  • Primary Citation of Related Structures:  
    6TED

  • PubMed Abstract: 
  • Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription ...

    Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitA1984Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1251Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit CC275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit DD142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit EE210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit FF127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit GG172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 10
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Uncharacterized proteinJ67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
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Entity ID: 11
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Uncharacterized proteinK117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 12
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Uncharacterized proteinL58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT6M1729Homo sapiensMutation(s): 0 
Gene Names: SUPT6HKIAA0162SPT6H
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Entity ID: 16
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RNA polymerase-associated protein CTR9 homologP [auth Q]1179Homo sapiensMutation(s): 0 
Gene Names: CTR9KIAA0155SH2BP1
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Entity ID: 17
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RNA polymerase-associated protein RTF1 homologQ [auth R]713Homo sapiensMutation(s): 0 
Gene Names: RTF1KIAA0252
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Entity ID: 19
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RNA polymerase-associated protein LEO1S [auth U]666Homo sapiensMutation(s): 0 
Gene Names: LEO1RDL
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Entity ID: 20
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RNA polymerase II-associated factor 1 homologT [auth V]531Homo sapiensMutation(s): 0 
Gene Names: PAF1PD2
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Entity ID: 21
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WD repeat-containing protein 61U [auth W]305Homo sapiensMutation(s): 0 
Gene Names: WDR61
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Entity ID: 22
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ParafibrominV [auth X]531Homo sapiensMutation(s): 0 
Gene Names: CDC73C1orf28HRPT2
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT4W [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT5X [auth Z]1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (37-MER)N 48synthetic construct
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Entity ID: 15
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')O [auth P]46synthetic construct
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Entity ID: 18
MoleculeChainsLengthOrganismImage
Template DNAR [auth T]48synthetic construct
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Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D 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: 3.10 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 CouncilGermany693023
German Research FoundationGermanySFB860
German Research FoundationGermanySFB860
Volkswagen FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release