4DM4 | pdb_00004dm4

The conserved domain of yeast Cdc73


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.265 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4DM4

This is version 1.1 of the entry. See complete history

Literature

Crystallographic analysis of the conserved C-terminal domain of transcription factor Cdc73 from Saccharomyces cerevisiae reveals a GTPase-like fold.

Chen, H.Shi, N.Gao, Y.Li, X.Teng, M.Niu, L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 953-959

  • DOI: https://doi.org/10.1107/S0907444912017325
  • Primary Citation Related Structures: 
    4DM4

  • PubMed Abstract: 

    The yeast Paf1 complex (Paf1C), which is composed of the proteins Paf1, Cdc73, Ctr9, Leo1 and Rtf1, accompanies RNA polymerase II from the promoter to the 3'-end formation site of mRNA- and snoRNA-encoding genes. As one of the first identified subunits of Paf1C, yeast Cdc73 (yCdc73) takes part in many transcription-related processes, including binding to RNA polymerase II, recruitment and activation of histone-modification factors and communication with other transcriptional activators. The human homologue of yCdc73, parafibromin, has been identified as a tumour suppressor linked to breast, renal and gastric cancers. However, the functional mechanism of yCdc73 has until recently been unclear. Here, a 2.2 Å resolution crystal structure of the highly conserved C-terminal region of yCdc73 is reported. It revealed that yCdc73 appears to have a GTPase-like fold. However, no GTPase activity was observed. The crystal structure of yCdc73 will shed new light on the modes of function of Cdc73 and Paf1C.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 40.24 kDa 
  • Atom Count: 2,785 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 73
A, B
167Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC73YLR418C
UniProt
Find proteins for Q06697 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06697 
Go to UniProtKB:  Q06697
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06697
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.265 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.938α = 90
b = 96.893β = 90
c = 114.029γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references