Crystal Structure Analysis of the UBF HMG box5

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Structure of human upstream binding factor HMG box 5 and site for binding of the cell-cycle regulatory factor TAF1

Rong, H.Li, Y.Shi, X.Zhang, X.Gao, Y.Dai, H.Teng, M.K.Niu, L.W.Liu, Q.Hao, Q.

(2007) Acta Crystallogr D Biol Crystallogr 63: 730-737

  • DOI: https://doi.org/10.1107/S0907444907017027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The fifth HMG-box domain in human upstream binding factor (hUBF) contributes to the synthesis of rRNA by RNA polymerase I (Pol I). The 2.0 A resolution crystal structure of this protein has been solved using the single-wavelength anomalous dispersion method (SAD). The crystal structure and the reported NMR structure have r.m.s. deviations of 2.18-3.03 A for the C(alpha) atoms. However, there are significant differences between the two structures, with displacements of up to 9.0 A. Compared with other HMG-box structures, the r.m.s. deviations for C(alpha) atoms between hUBF HMG box 5 and HMG domains from Drosophila melanogaster protein D and Rattus norvegicus HMG1 are 1.5 and 1.6 A, respectively. This indicates that the differences between the crystal and NMR structures of hUBF HMG box 5 are larger than those with its homologous structures. The differences between the two structures potentially reflect two states with different structures. The specific interactions between the hUBF HMG box 5 and the first bromodomain of TBP-associated factor 1 (TAF1) were studied by ultrasensitive differential scanning calorimetry and chemical shift perturbation. Based on these experimental data, possible sites in hUBF HMG box 5 that may interact with the first bromodomain of TAF1 were proposed.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar transcription factor 191Homo sapiensMutation(s): 0 
Gene Names: UBF
UniProt & NIH Common Fund Data Resources
Find proteins for P17480 (Homo sapiens)
Explore P17480 
Go to UniProtKB:  P17480
PHAROS:  P17480
GTEx:  ENSG00000108312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17480
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.812α = 90
b = 60.812β = 90
c = 63.158γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references