|Entry||Database: EMDB / ID: EMD-22477|
|Title||Cryo-EM map of the human BAF-nucleosome complex refined with a mask for the nucleosome|
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 5.6 Å|
|Authors||Suzuki H / Mashtalir N / Kadoch C / Walz T|
|Funding support|| United States, 1 items |
|Citation||Journal: Cell / Year: 2020|
Title: A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms.
Authors: Nazar Mashtalir / Hiroshi Suzuki / Daniel P Farrell / Akshay Sankar / Jie Luo / Martin Filipovski / Andrew R D'Avino / Roodolph St Pierre / Alfredo M Valencia / Takashi Onikubo / Robert G ...Authors: Nazar Mashtalir / Hiroshi Suzuki / Daniel P Farrell / Akshay Sankar / Jie Luo / Martin Filipovski / Andrew R D'Avino / Roodolph St Pierre / Alfredo M Valencia / Takashi Onikubo / Robert G Roeder / Yan Han / Yuan He / Jeffrey A Ranish / Frank DiMaio / Thomas Walz / Cigall Kadoch /
Abstract: Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate genomic architecture. Here, we present a structural model of the endogenously purified human canonical BAF ...Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate genomic architecture. Here, we present a structural model of the endogenously purified human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy (cryo-EM), cross-linking mass spectrometry, and homology modeling. BAF complexes bilaterally engage the nucleosome H2A/H2B acidic patch regions through the SMARCB1 C-terminal α-helix and the SMARCA4/2 C-terminal SnAc/post-SnAc regions, with disease-associated mutations in either causing attenuated chromatin remodeling activities. Further, we define changes in BAF complex architecture upon nucleosome engagement and compare the structural model of endogenous BAF to those of related SWI/SNF-family complexes. Finally, we assign and experimentally interrogate cancer-associated hot-spot mutations localizing within the endogenous human BAF complex, identifying those that disrupt BAF subunit-subunit and subunit-nucleosome interfaces in the nucleosome-bound conformation. Taken together, this integrative structural approach provides important biophysical foundations for understanding the mechanisms of BAF complex function in normal and disease states.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_22477.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.699 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire BAF-nucleosome complex
|Entire||Name: BAF-nucleosome complex / Number of components: 1|
-Component #1: protein, BAF-nucleosome complex
|Protein||Name: BAF-nucleosome complex / Recombinant expression: No|
|Mass||Theoretical: 1.4 MDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Imaging||Microscope: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 69 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 14841|
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