2HDZ

Crystal Structure Analysis of the UBF HMG box5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.,Sect.D 63: 730-737

  • DOI: 10.1107/S0907444907017027

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleolar transcription factor 1
A
91Homo sapiensMutation(s): 0 
Gene Names: UBTF (UBF, UBF1)
Find proteins for P17480 (Homo sapiens)
Go to Gene View: UBTF
Go to UniProtKB:  P17480
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 60.812α = 90.00
b = 60.812β = 90.00
c = 63.158γ = 120.00
Software Package:
Software NamePurpose
RESOLVEphasing
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
ADSCdata collection
REFMACrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description