2HDZ: Crystal Structure Analysis Of The Ubf Hmg Box5

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.
PDB ID: 2HDZDownload
MMDB ID: 47127
PDB Deposition Date: 2006/6/21
Updated in MMDB: 2010/12
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
Similar Structures:
Biological Unit for 2HDZ: monomeric; determined by author
Molecular Components in 2HDZ
Label Count Molecule
Protein (1 molecule)
Nucleolar Transcription Factor 1(Gene symbol: UBTF)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB