Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling

Koliopoulos, Marios G.; Muhammad, Reyhan; Roumeliotis, Theodoros I.; Beuron, Fabienne; Choudhary, Jyoti S.; Alfieri, Claudio

doi:10.1038/s41467-022-32798-9

Cited by 11 publications

(12 citation statements)

References 71 publications

(110 reference statements)

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“…These particles were piped into the “ab initio model” function implemented in cryoSPARC. These particles were then imported in RELION-3.1.1 70 as described in 71 Refinement, Bayesian polishing was performed as in ref. 71 and as illustrated in the Supplementary Figs.…”

Section: Methodsmentioning

confidence: 99%

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Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex

et al. 2023

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Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.

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Section: Methodsmentioning

confidence: 99%

“…These particles were then imported in RELION-3.1.1 70 as described in 71 Refinement, Bayesian polishing was performed as in ref. 71 and as illustrated in the Supplementary Figs. 2 , 3 and 4.…”

Section: Methodsmentioning

confidence: 99%

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex

et al. 2023

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“…Sequences of an organism not contained within the analyzed sample are added to the database for search in order to estimate the FDR among the target hits after target-decoy validation. Several publications have shown that this can also be applied to XLMS for validating cross-linking results. ,, We used the proteome of E. coli for entrapment as there was no E.…”

Section: Methodsmentioning

confidence: 99%

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity

Birklbauer,

Matzinger,

Müller

et al. 2023

J. Proteome Res.

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Cross-linking mass spectrometry has become a powerful tool for the identification of protein–protein interactions and for gaining insight into the structures of proteins. We previously published MS Annika, a cross-linking search engine which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable cross-linkers. In this publication, we present MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level, only supports the processing of data from MS2–MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Detected cross-links are validated by estimating the false discovery rate (FDR) using a target-decoy approach. We evaluated the MS3-search-capabilities of MS Annika 2.0 on five different datasets covering a variety of experimental approaches and compared it to XlinkX and MaXLinker, two other cross-linking search engines. We show that MS Annika detects up to 4 times more true unique cross-links while simultaneously yielding less false positive hits and therefore a more accurate FDR estimation than the other two search engines. All mass spectrometry proteomics data along with result files have been deposited to the ProteomeXchange consortium via the PRIDE partner repository with the dataset identifier PXD041955.

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“…https://doi.org/10.5281/zenodo.3576630. Refinement, Bayesian polishing was performed as in 69 . Further map improvement was performed by performing 3D classification without alignment (T=30) with a soft mask on the SIN3B core subcomplex and performing Ctf refinement in RELION.…”

Section: Sin3b-apo Complexmentioning

confidence: 99%

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex

Muhammad

Koliopoulos

Roumeliotis

et al. 2023

Preprint

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Histone deacetylase complexes remove histone lysine acetylation, a key post-translational modification that activates transcription at each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the first structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.

show abstract

Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling

Cited by 11 publications

References 71 publications

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex

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