2HDZ

Crystal Structure Analysis of the UBF HMG box5

Summary for 2HDZ

• Entry DOI: 10.2210/pdb2hdz/pdb
• Descriptor: Nucleolar transcription factor 1 (2 entities in total)
• Functional Keywords: hmg domain, protein binding
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus, nucleolus : P17480
• Total number of polymer chains: 1
• Total formula weight: 10891.57

Authors

Rong, H.,Teng, M.K.,Niu, L.W. (deposition date: 2006-06-21, release date: 2007-06-26, Last modification date: 2024-03-13)

Primary citation

Rong, H.,Li, Y.,Shi, X.,Zhang, X.,Gao, Y.,Dai, H.,Teng, M.K.,Niu, L.W.,Liu, Q.,Hao, Q.
Structure of human upstream binding factor HMG box 5 and site for binding of the cell-cycle regulatory factor TAF1
Acta Crystallogr.,Sect.D, 63:730-737, 2007

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.

PubMed: 17505112
DOI: 10.1107/S0907444907017027

Experimental method

X-RAY DIFFRACTION (2 Å)