6UCH | pdb_00006uch

SMARCB1 nucleosome-interacting C-terminal alpha helix

• PDB DOI: https://doi.org/10.2210/pdb6UCH/pdb
• BMRB: 30672

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-16 Released: 2019-11-27 
• Deposition Author(s): Valencia, A.M., Sun, Z.Y.J., Seo, H.S., Vangos, H.S., Yeoh, Z.C., Mashtalir, N., Dhe-Paganon, S., Kadoch, C.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling.

Valencia, A.M., Collings, C.K., Dao, H.T., St Pierre, R., Cheng, Y.C., Huang, J., Sun, Z.Y., Seo, H.S., Mashtalir, N., Comstock, D.E., Bolonduro, O., Vangos, N.E., Yeoh, Z.C., Dornon, M.K., Hermawan, C., Barrett, L., Dhe-Paganon, S., Woolf, C.J., Muir, T.W., Kadoch, C.

(2019) Cell 179: 1342-1356.e23

• PubMed: 31759698 
• DOI: https://doi.org/10.1016/j.cell.2019.10.044
• Primary Citation Related Structures: 
  6UCH


• PubMed Abstract: 
  

  Mammalian switch/sucrose non-fermentable (mSWI/SNF) complexes are multi-component machines that remodel chromatin architecture. Dissection of the subunit- and domain-specific contributions to complex activities is needed to advance mechanistic understanding. Here, we examine the molecular, structural, and genome-wide regulatory consequences of recurrent, single-residue mutations in the putative coiled-coil C-terminal domain (CTD) of the SMARCB1 (BAF47) subunit, which cause the intellectual disability disorder Coffin-Siris syndrome (CSS), and are recurrently found in cancers. We find that the SMARCB1 CTD contains a basic α helix that binds directly to the nucleosome acidic patch and that all CSS-associated mutations disrupt this binding. Furthermore, these mutations abrogate mSWI/SNF-mediated nucleosome remodeling activity and enhancer DNA accessibility without changes in genome-wide complex localization. Finally, heterozygous CSS-associated SMARCB1 mutations result in dominant gene regulatory and morphologic changes during iPSC-neuronal differentiation. These studies unmask an evolutionarily conserved structural role for the SMARCB1 CTD that is perturbed in human disease.

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Organizational Affiliation: 
• Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology Program, Harvard University, Cambridge, MA 02138, USA.
Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.75 kDa 
• Atom Count: 329 
• Modeled Residue Count: 41 
• Deposited Residue Count: 41 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	A	41	Homo sapiens	Mutation(s): 0  Gene Names: SMARCB1, BAF47, INI1, SNF5L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12824 (Homo sapiens) Explore Q12824  Go to UniProtKB:  Q12824
PHAROS:  Q12824 GTEx:  ENSG00000099956

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Valencia, A.M., Sun, Z.Y.J., Seo, H.S., Vangos, H.S., Yeoh, Z.C., Mashtalir, N., Dhe-Paganon, S., Kadoch, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	--

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references