1,720,996 research outputs found
Sequencing data for Flp-In T-Rex HeLa PINK1 CRISPR/CAS9 knock-out (CVCL_D5JI)
No full text<p>PCR and sequencing data (.ab1 and .seq files) for CRISPR-Cas9 PINK1 knockout HeLa cells (clone 3C9) described in <a title="doi link" href="https://doi.org/10.1098/rsob.210264">doi.org/10.1098/rsob.210264</a>. Knock-out generated using the following guides (targeting exone 2), available from MRC-PPU Reagents and Services, University of Dundee: DU52528 and DU52530 (CRISPR Project #CR252). This cell line has been deposited to Cellosaurus: CVCL_D5JI.</p>
Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3
No full textCrystal structures were deposited to the PDB with the following accession number: K48–K63-branched Ub3 in complex with NbSL3 (PDB 7NBB
LC-MS/MS analysis of ribosome UFMylation in vitro
No full textUFMylation, is a Ubiquitin-like modification occurring on RPL26, a ribosomal subunit, upon ribosome stalling at the ER membrane. This modification is achieved by a pool of enzymes commonly referred to as E1-activating, E2-conjugating and E3-ligase enzymes. The UFM1 E3 ligase comprises of three proteins: UFL1, UFBP1 and CDK5RAP3, referred to as UFM1 Ribosome E3 Ligase (UREL) complex. While UFL1 and UFBP1 are sufficient for E3 ligase activity in vitro, CDK5RAP3 is indispensable for ribosome UFMylation in vivo. In this work, we characterize in vitro UFMylation reaction of purified 60S ribosomes in the presence and absence of CDK5RAP3 using LC-MS/MS. Specifically, we analyse sites of UFMylation, linkage type and quantify monoUFMylation and diUFMylation on RPL26. Interestingly, we find UFMylation to occur on a specific lysine residue, K134, in the presence of UFL1/UFBP1 alone and in complex with CDK5RAP3. In addition, we also provide quantitative information on relative abundances of RPL26 mono- and di-UFMylation under these conditions
UFL1 E3 ligase bound 60S ribosome
No full textThe cryo-EM coordinates have been deposited at the PDB under accession code 8QFC (ligase only)
UFL1/DDRG1 bound to UFC1
No full textX-ray structure factors and associated models have been deposited at the PDB under accession code 8C0
K48-K63-Ubiquitin chain pulldown from U2OS cell lysates
No full textSpyTagged branched and unbranched K48- and K63-linked Tetra-Ubiquitin chains were immobilized on SpyCatcher agarose (48Ub4; 63Ub4; [Ub]2-48,63Ub-48Ub; [Ub]2-48,63Ub-63Ub). Pulldown were performed from protease-inhibitor treated U2OS cell lines to identify specific binders of K48-K63-branched Ub4
Branched K48-K63-Ub3
No full textCrystal structures were deposited to the PDB with the following accession number: K48–K63-branched Ub3 (PDB 7NPO
UFC1-UFM1 conjugate
No full textX-ray structure factors and associated models have been deposited at the PDB under accession code 8BZ
UFL1 E3 ligase bound 60S ribosome
No full textThe cryo-EM coordinates have been deposited at the PDB under accession code 8QFD (ligase-bound 60S)
Mechanism of 60S ribosomal subunit recognition and UFMylation by the UFM1 E3 ligase complex
No full textDuring co-translational translocation at the endoplasmic reticulum (ER), ribosomes can stall and become covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit RPL26 (uL24). This process, known as UFMylation, is mediated by the UFM1 Ribosome E3 Ligase (UREL) complex, comprised of UFL1, UFBP1, and CDK5RAP3. However, the functional consequences of UFMylation and catalytic mechanisms of UREL are unknown. Here, we present crosslinking-mass spectrometry (XL-MS) data of UREL bound to 60S ribosomes
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