7DKH

Crystal structure of the Ctr9/Paf1/Cdc73/Rtf1 quaternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of the Core Module of the Yeast Paf1 Complex.

Chen, F.L.Liu, B.B.Zeng, J.W.Guo, L.Ge, X.Feng, W.Li, D.F.Zhou, H.Long, J.F.

(2021) J Mol Biol 434: 167369-167369

  • DOI: https://doi.org/10.1016/j.jmb.2021.167369
  • Primary Citation of Related Structures:  
    7DKH

  • PubMed Abstract: 

    The highly conserved multifunctional polymerase-associated factor 1 (Paf1) complex (PAF1C), which consists of five core subunits: Ctr9, Paf1, Leo1, Cdc73, and Rtf1, acts as a diverse hub that regulates all stages of RNA polymerase II-mediated transcription and various other cellular functions. However, the underlying mechanisms remain unclear. Here, we report the crystal structure of the core module derived from a quaternary Ctr9/Paf1/Cdc73/Rtf1 complex of S. cerevisiae PAF1C, which reveals interfaces between the tetratricopeptide repeat module in Ctr9 and Cdc73 or Rtf1, and find that the Ctr9/Paf1 subcomplex is the key scaffold for PAF1C assembly. Our study demonstrates that Cdc73 binds Ctr9/Paf1 subcomplex with a very similar conformation within thermophilic fungi or human PAF1C, and that the binding of Cdc73 to PAF1C is important for yeast growth. Importantly, our structure reveals for the first time that the extreme C-terminus of Rtf1 adopts an "L"-shaped structure, which interacts with Ctr9 specifically. In addition, disruption of the binding of either Cdc73 or Rtf1 to PAF1C greatly affects the normal level of histone H2B K123 monoubiquitination in vivo. Collectively, our results provide a structural insight into the architecture of the quaternary Ctr9/Paf1/Cdc73/Rtf1 complex and PAF1C functional regulation.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9
A, E, I
972Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTR9CDP1YOL145C
UniProt
Find proteins for P89105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P89105
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP89105
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated protein 1
B, F, J
103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAF1YBR279WYBR2016
UniProt
Find proteins for P38351 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38351
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UniProt GroupP38351
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 73
C, G, K
57Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC73YLR418C
UniProt
Find proteins for Q06697 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q06697
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UniProt GroupQ06697
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1
D, H, L
68Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTF1CSL3YGL244WHRA458
UniProt
Find proteins for P53064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53064 
Go to UniProtKB:  P53064
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UniProt GroupP53064
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, E, I
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.195α = 90
b = 190.195β = 90
c = 216.423γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31670758
National Natural Science Foundation of China (NSFC)China31870750

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-01-05
    Changes: Database references