1V81

Solution structures of ubiquitin at 30 bar and 3 kbar

Summary for 1V81

• Entry DOI: 10.2210/pdb1v81/pdb
• Related: 1V80
• Descriptor: Ubiquitin/60s ribosomal protein L40 fusion (1 entity in total)
• Functional Keywords: pressure, signaling protein, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi
• Biological source: Bos taurus (cattle)
• Total number of polymer chains: 1
• Total formula weight: 8576.83

Authors

Kitahara, R.,Yokoyama, S.,Akasaka, K.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-12-27, release date: 2005-02-15, Last modification date: 2023-12-27)

Primary citation

Kitahara, R.,Yokoyama, S.,Akasaka, K.
NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.
J.Mol.Biol., 347:277-285, 2005

PubMed Abstract: Conformational fluctuation plays a key role in protein function, but we know little about the associated structural changes. Here we present a general method for elucidating, at the atomic level, a large-scale shape change of a protein molecule in solution undergoing conformational fluctuation. The method utilizes the intimate relationship between conformation and partial molar volume and determines three-dimensional structures of a protein at different pressures using variable pressure NMR technique, whereby NOE distance and torsion angle constraints are used to create average coordinates. Ubiquitin (pH 4.6 at 20 degrees C) was chosen as the first target, for which structures were determined at 30 bar and at 3 kbar, giving "NMR snapshots" of a fluctuating protein structure at atomic resolution. The result reveals that the helix swings in and out by >3 angstroms with a simultaneous reorientation of the C-terminal segment, providing an "open" conformer suitable for enzyme recognition. Spin relaxation analysis indicates that this fluctuation occurs in the ten microsecond time range with activation volumes -4.2(+/-3.2) and 18.5(+/-3.0) ml/mol for the "closed-to-open" and the "open-to-closed" transitions, respectively.

PubMed: 15740740
DOI: 10.1016/j.jmb.2005.01.052

Experimental method

SOLUTION NMR