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



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 repo ...

    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 ╬▒-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, G├Âttingen, Germany. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit GG172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
Find proteins for P60899 (Sus scrofa)
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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: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinJ67Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinK117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
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
Find proteins for Q7KZ85 (Homo sapiens)
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PHAROS  Q7KZ85
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9 homologQ1179Homo sapiensMutation(s): 0 
Gene Names: CTR9KIAA0155SH2BP1
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PHAROS  Q6PD62
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1 homologR713Homo sapiensMutation(s): 0 
Gene Names: RTF1KIAA0252
Find proteins for Q92541 (Homo sapiens)
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PHAROS  Q92541
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein LEO1U666Homo sapiensMutation(s): 0 
Gene Names: LEO1RDL
Find proteins for Q8WVC0 (Homo sapiens)
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PHAROS  Q8WVC0
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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
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Entity ID: 20
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RNA polymerase II-associated factor 1 homologV531Homo sapiensMutation(s): 0 
Gene Names: PAF1PD2
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PHAROS  Q8N7H5
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 61W305Homo sapiensMutation(s): 0 
Gene Names: WDR61
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PHAROS  Q9GZS3
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
ParafibrominX531Homo sapiensMutation(s): 0 
Gene Names: CDC73C1orf28HRPT2
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PHAROS  Q6P1J9
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Y121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
Find proteins for P63272 (Homo sapiens)
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PHAROS  P63272
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT5Z1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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PHAROS  O00267
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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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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  • Reference Sequence
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Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (37-MER)N48synthetic 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')P46synthetic construct
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Entity ID: 18
MoleculeChainsLengthOrganismImage
Template DNAT48synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, I, J, L, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-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

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany693023
German Research FoundationGermanySFB860
German Research FoundationGermanySFB860
Volkswagen FoundationGermany--

Revision History 

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