3U30

Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin

Summary for 3U30

• Entry DOI: 10.2210/pdb3u30/pdb
• Related: 1UBQ 3DVG
• Descriptor: linear di-ubiquitin, Light chain Fab, Heavy chain Fab, ... (4 entities in total)
• Functional Keywords: immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Ubiquitin: Cytoplasm : P0CG48
• Total number of polymer chains: 6
• Total formula weight: 133357.73

Authors

Matsumoto, M.L.,Dong, K.C.,Yu, C.,Phu, L.,Gao, X.,Hannoush, R.N.,Hymowitz, S.G.,Kirkpatrick, D.S.,Dixit, V.M.,Kelley, R.F. (deposition date: 2011-10-04, release date: 2012-01-18, Last modification date: 2024-11-06)

Primary citation

Matsumoto, M.L.,Dong, K.C.,Yu, C.,Phu, L.,Gao, X.,Hannoush, R.N.,Hymowitz, S.G.,Kirkpatrick, D.S.,Dixit, V.M.,Kelley, R.F.
Engineering and structural characterization of a linear polyubiquitin-specific antibody.
J.Mol.Biol., 418:134-144, 2012

PubMed Abstract: Polyubiquitination is an essential posttranslational modification that plays critical roles in cellular signaling. PolyUb (polyubiquitin) chains are formed by linking the carboxyl-terminus of one Ub (ubiquitin) subunit to either a lysine residue or the amino-terminus of an adjacent Ub. Linkage through the amino-terminus results in linear polyubiquitination that has recently been demonstrated to be a key step in nuclear factor κB activation; however, tools to study linear chains have been lacking. We therefore engineered a linear-linkage-specific antibody that is functional in Western blot, immunoprecipitation, and immunofluorescence applications. A crystal structure of the linear-linkage-specific antibody Fab fragment in complex with linear diubiquitin provides molecular insight into the nature of linear chain specificity. We use the antibody to demonstrate that linear polyUb is up-regulated upon tumor necrosis factor α stimulation of cells, consistent with a critical role in nuclear factor κB signaling. This antibody provides an essential tool for further investigation of the function of linear chains.

PubMed: 22227388
DOI: 10.1016/j.jmb.2011.12.053

Experimental method

X-RAY DIFFRACTION (2.428 Å)