xiNET: Cross-link Network Maps With Residue Resolution

Combe, Colin; Fischer, Lutz; Rappsilber, Juri

doi:10.1074/mcp.o114.042259

Cited by 272 publications

(250 citation statements)

References 26 publications

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“…All displayed cross‐links have LD (linear‐discriminant) confidence score at least 23, as calculated by xQuest (Leitner et al , 2014). The figure was created with xiNET (Combe et al , 2015). …”

Section: Resultsmentioning

confidence: 99%

Structural insights into transcription initiation by yeast RNA polymerase I

et al. 2017

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In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre‐rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi‐subunit pre‐initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo‐EM structure of the 18‐subunit yeast Pol I PIC bound to a transcription scaffold. The cryo‐EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB‐related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.

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Section: Resultsmentioning

confidence: 99%

Structural insights into transcription initiation by yeast RNA polymerase I

et al. 2017

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“…Protein regions not present in the crystal structures and homology models are colored black. Figure was drawn using xi NET 76.…”

Section: Resultsmentioning

confidence: 99%

Architecture of the yeast Elongator complex

et al. 2016

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The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1‐6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub‐complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two‐lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.

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“…The final best 200 solutions according to HADDOCK score were used for analysis and display. All the crosslinking maps were generated with xiNET (46). All the interaction networks were generated with Cytoscape (47).…”

Section: Discussionmentioning

confidence: 99%

Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei

Fasci

Ingen

Scheltema

et al. 2018

Molecular & Cellular Proteomics

119

111

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Cells organize their actions partly through tightly controlled protein-protein interactionscollectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the protein-protein interactions in intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links connecting distinct proteins. From this data, we gain insights on interactions involving histone proteins. We observed that core histones on the nucleosomes expose well-defined interaction hot spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build low-resolution models of their binding mode to the nucleosome. For HMGN2 the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS and modeling. Excitingly, the analysis of crosslinks carrying post-translational modifications allowed us to extract how specific modifications influence nucleosome interactions. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.

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xiNET: Cross-link Network Maps With Residue Resolution

Cited by 272 publications

References 26 publications

Structural insights into transcription initiation by yeast RNA polymerase I

Structural insights into transcription initiation by yeast RNA polymerase I

Architecture of the yeast Elongator complex

Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei

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