Insight into the Architecture of the NuRD Complex
Open accessAbstract
The nucleosome remodeling and deacetylase (NuRD) complex is a widely conserved transcriptional co-regulator that harbors both nucleosome remodeling and histone deacetylase activities. It plays a critical role in the early stages of ES cell differentiation and the reprogramming of somatic to induced pluripotent stem cells. Abnormalities in several NuRD proteins are associated with cancer and aging. We have investigated the architecture of NuRD by determining the structure of a subcomplex comprising RbAp48 and MTA1. Surprisingly, RbAp48 recognizes MTA1 using the same site that it uses to bind histone H4, showing that assembly into NuRD modulates RbAp46/48 interactions with histones. Taken together with other results, our data show that the MTA proteins act as scaffolds for NuRD complex assembly. We further show that the RbAp48-MTA1 interaction is essential for the in vivo integration of RbAp46/48 into the NuRD complex.
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None of these studies described comprehensive protein structures for both binding partners, so the complete interaction interfaces remain unknown.
“None of these studies described comprehensive protein structures for both binding partners, so the complete interaction interfaces remain unknown.”
From Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics (2015) · cites this paper as [20]
The Results (page unavailable) describe crystal structures of RbAp48 bound to short MTA1 peptides, not comprehensive structures of both full-length binding partners. They also identify contacts at the peptide-binding interface. The paper therefore supports the structural limitation, but not an unqualified assertion that the interaction interface remains unknown or that none of the other studies resolved it. (LLM, conf=0.82)
Experimental — accuracy not yet measuredFew NuRD subcomplexes have resolved structures, most notably the MBD2-GATAD2A coiled-coil subcomplex, the RBBP4-MTA1 subcomplex, and the HDAC1-MTA1 subcomplex.
“Few NuRD subcomplexes have resolved structures, most notably the MBD2 -GATAD2A coiled-coil subcomplex, the RBBP4 -MTA1 subcomplex, and the HDAC1 -MTA1 subcomplex [20,29,30].”
RBBP4 and RBBP7 dynamic behavior is in agreement with recent structural studies suggesting that MTA and histone H4 compete for RBBP binding.
“These observations are in agreement with recent structural studies suggesting that MTA and histone H4 compete for RBBP binding [20].”
Mapping cross-linked residues onto known RBBP4 structure shows Lys25 and Lys307 fall on either side of the known MTA1 interaction interface (PDB 4PC0).
“mapping cross-linked residues onto the known RBBP4 structure shows that Lys25 and Lys307 fall on either side of the known MTA1 interaction interface (PDB 4PC0 [20]) (Fig. 4A).”
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Exploration of the HDAC2 foot pocket: Synthesis and SAR of substituted N-(2-aminophenyl)benzamides
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“There are three-dimensional structures available for two intact subunits, namely RbAp46/48 (16, 17) and HDAC2/HDAC1 (26, 27).”
BackgroundSmits, A. H., Jansen, P. W. T. C., Poser, I., Hyman, A. A., & Vermeulen, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks941 · Cited by 258 · see citing works
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Molecular Mechanism for Age-Related Memory Loss: The Histone-Binding Protein RbAp48
Pavlopoulos, E., Jones, S., Kosmidis, S., Close, M., Kim, C., Kovalerchik, O., Small, S. A., & Kandel, E. R. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3006373 · Cited by 109 · cited 1× · see citing works
“A role for RbAp48 as a mediator of age-related memory loss has also recently been reported (19).”
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- Authors
- Alqarni, S. S. M., Murthy, A., Zhang, W., Przewloka, M. R., Silva, A. P. G., Watson, A. A., Lejon, S., Pei, X. Y., Smits, A. H., Kloet, S. L., Wang, H., Shepherd, N. E., Stokes, P. H., Blobel, G. A., Vermeulen, M., Glover, D. M., Mackay, J. P., & Laue, E. D.
- Affiliations
- The University of Sydney (AU)
- University of Cambridge (GB)
- University Medical Center Utrecht (NL)
- Children's Hospital of Philadelphia (US)
- Corresponding author
- Mackay, Joel P.
- Laue, Ernest D.
- ORCID
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2014-08
- Volume
- 289
- Issue
- 32
- Pages
- 21844-21855
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC4139204
- OpenAlex
- W1975098321
- Cited by
- 84
- References
- 5
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 1 · 2023: 5 · 2022: 5 · 2021: 2 · 2020: 10 · 2019: 9 · 2018: 10 · 2017: 9 · 2016: 9 · 2015: 9 · 2014: 7
- FWCI
- 4.65
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- National Institutes of Health (OD010949-10)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- NuRD complex, RbAp48, MTA1, complex architecture, histone deacetylase, nucleosome remodeling, protein-protein interaction, complex assembly, transcriptional coregulators, induced pluripotent stem cells, somatic cell reprogramming
- MeSH terms
- Amino Acid Sequence, Animals, Histone Deacetylases, Histones, Humans, Models, Molecular, Molecular Sequence Data, Nuclear Proteins, Nucleosomes, Repressor Proteins, Transcription Factors, Trans-Activators, Conserved Sequence, Sequence Homology, Amino Acid, Crystallography, X-Ray, Chromatin Assembly and Disassembly, Protein Interaction Domains and Motifs, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Retinoblastoma-Binding Protein 4, Retinoblastoma-Binding Protein 7
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