+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31217 | |||||||||
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Title | The structure of ALC1 bound to the nucleosome | |||||||||
Map data | The structure of ALC1 bound to the nucleosome | |||||||||
Sample |
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Function / homology | Function and homology information poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / site of DNA damage / nucleosome binding / DNA helicase activity / histone reader activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin ...poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / site of DNA damage / nucleosome binding / DNA helicase activity / histone reader activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / chromatin remodeling / protein heterodimerization activity / DNA repair / nucleotide binding / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Chen ZC / Chen KJ / Wang L | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of ALC1/CHD1L autoinhibition and the mechanism of activation by the nucleosome. Authors: Li Wang / Kangjing Chen / Zhucheng Chen / Abstract: Chromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is ...Chromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is regulated remain unclear. Here we report the crystal structure of human ALC1 and the cryoEM structure bound to the nucleosome. The structure shows the macro domain of ALC1 binds to lobe 2 of the ATPase motor, sequestering two elements for nucleosome recognition, explaining the autoinhibition mechanism of the enzyme. The H4 tail competes with the macro domain for lobe 2-binding, explaining the requirement for this nucleosomal epitope for ALC1 activation. A dual-arginine-anchor motif of ALC1 recognizes the acidic pocket of the nucleosome, which is critical for chromatin remodeling in vitro. Together, our findings illustrate the structures of ALC1 and shed light on its regulation mechanisms, paving the way for the discovery of drugs targeting ALC1 for the treatment of cancer. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31217.map.gz | 24.3 MB | EMDB map data format | |
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Header (meta data) | emd-31217-v30.xml emd-31217.xml | 23.5 KB 23.5 KB | Display Display | EMDB header |
Images | emd_31217.png | 121.4 KB | ||
Masks | emd_31217_msk_1.map emd_31217_msk_2.map | 421.9 MB 421.9 MB | Mask map | |
Others | emd_31217_additional_1.map.gz emd_31217_additional_2.map.gz | 20.9 MB 8.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31217 | HTTPS FTP |
-Validation report
Summary document | emd_31217_validation.pdf.gz | 390.1 KB | Display | EMDB validaton report |
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Full document | emd_31217_full_validation.pdf.gz | 389.7 KB | Display | |
Data in XML | emd_31217_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_31217_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31217 | HTTPS FTP |
-Related structure data
Related structure data | 7ennMC 7epuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31217.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The structure of ALC1 bound to the nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.54125 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31217_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_31217_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: The structure of ALC1 linker region bound to the nucleosome
File | emd_31217_additional_1.map | ||||||||||||
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Annotation | The structure of ALC1 linker region bound to the nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The structure of ALC1 motor domain
File | emd_31217_additional_2.map | ||||||||||||
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Annotation | The structure of ALC1 motor domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The structure of ALC1 bound to the nucleosome
+Supramolecule #1: The structure of ALC1 bound to the nucleosome
+Supramolecule #2: ALC1
+Supramolecule #3: Histone
+Supramolecule #4: DNA
+Macromolecule #1: Chromodomain-helicase-DNA-binding protein 1-like
+Macromolecule #2: Histone H3.2
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A type 1
+Macromolecule #5: Histone H2B 1.1
+Macromolecule #6: DNA (167-MER)
+Macromolecule #7: DNA (167-MER)
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 586673 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |