Evidence map›Paper›PMID 42680104›Full record

ArticleMolecular & cellular proteomics : MCP2026

Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.

Jules Nde, Kartik Majila, Rosalyn C Zimmermann, Cassandra Kempf, Ying Zhang, Joseph Cesare, Janet L Thornton, Jerry L Workman, Laurence Florens, Shruthi Viswanath and 1 more

Abstract read
In one paragraph

Article in Molecular & cellular proteomics : MCP, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Jules NdeDepartment of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
Kartik MajilaNational Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
Rosalyn C ZimmermannDepartment of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
Cassandra KempfStowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Chemistry, The Center of Mass Spectrometry and Metabolic Tracing, Washington University St Louis, St Louis, Missouri, USA.
Ying ZhangStowers Institute for Medical Research, Kansas City, Missouri, USA.
Joseph CesareDepartment of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Stowers Institute for Medical Research, Kansas City, Missouri, USA.
Janet L ThorntonDepartment of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
Jerry L WorkmanStowers Institute for Medical Research, Kansas City, Missouri, USA.
Laurence FlorensStowers Institute for Medical Research, Kansas City, Missouri, USA.
Shruthi ViswanathNational Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India. Electronic address: shruthiv@ncbs.res.in.
Michael P WashburnDepartment of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas, USA. Electronic address: mwashburn4@kumc.edu.

Funding

Transcription regulation in chromatinR35GM118068 · NIGMS · STOWERS INSTITUTE FOR MEDICAL RESEARCH · PI JERRY L WORKMAN · 2016 to 2026
$4.2M
Decoding the Assembly and Function of Paralogue Specific SIN3A and SIN3B Human Chromatin Remodeling Complexes and NetworksR35GM145240 · NIGMS · UNIVERSITY OF KANSAS MEDICAL CENTER · PI MICHAEL P WASHBURN · 2022 to 2026
$1.9M
Kansas Medical Scientist Training ProgramT32GM138077 · NIGMS · UNIVERSITY OF KANSAS MEDICAL CENTER · PI TIMOTHY A FIELDS · 2020 to 2026
$1.6M
Deciphering the Paralogue Specific Interactions within the Sin3 Protein Interaction NetworkF31GM131536 · NIGMS · STOWERS INSTITUTE FOR MEDICAL RESEARCH · PI KEMPF, CASSANDRA G · 2019 to 2020
$51k
NIGMS NIH HHS F31 GM131536NIGMS NIH HHS R35 GM118068NIGMS NIH HHS R35 GM145240NIGMS NIH HHS T32 GM138077
6 · The paper itself

Abstract

Histone Deacetylase (HDAC) 1 and 2 are key enzymatic components in multiple large chromatin remodeling complexes including NuRD, SIN3, and CoREST. In addition, both HDAC 1 and 2 contain a large intrinsically disordered region (IDR) within their C-terminal domain (CTD). How HDAC1/2 assemble into these complexes and the structure of the CTD IDR remains poorly understood. Here, we used HDAC1/2 to isolate their protein interaction networks from cells and used crosslinking mass spectrometry coupled with the Integrative Modeling Platform to build structural models of the NuRD, SIN3A, and CoREST complexes. Next, we implemented an AlphaFold-enabled crosslinking mass spectrometry constrained modeling approach to investigate how HDAC1 could assemble into these complexes. We show that the CTD IDR of HDAC1 folds into alpha helices in these complexes. Finally, we built a complete integrative structural model of a NuRD subcomplex including the abundant HDAC1:MBD3:MTA1:GATAD2B:RBBP4 subunits, which included 6 IDRs. The approaches used herein are broadly applicable for the study of protein complexes and protein interaction networks that can provide important insights into IDRs.

Indexed as

CoRESTcrosslinking mass spectrometryendogenous complex structuresHDAC1HDAC2integrative structural modelingintrinsically disordered regionsNuRDSIN3A

Identifiers

PMID42680104
PMCPMC13676700

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.