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Yorodumi- EMDB-11221: Cryo-EM structure of the regulatory linker of ALC1 bound to the n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11221 | |||||||||
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Title | Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. | |||||||||
Map data | Map filtered by local resolution from RELION LocalRes procedure. | |||||||||
Sample |
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Keywords | ALC1 / CHD1L / chromatin remodeler / DNA damage response / nucleosome / hexasome / NUCLEAR PROTEIN / GENE REGULATION / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / histone reader activity / site of DNA damage / nucleosome binding / DNA helicase 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 / histone reader activity / site of DNA damage / nucleosome binding / DNA helicase 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 | Xenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Bacic L / Gaullier G / Deindl S | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Authors: Croll TI #3: Journal: IUCrJ / Year: 2020 Title: Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in Authors: Zivanov J / Nakane T / Scheres SHW #4: Journal: J. Struct. Biol. / Year: 2012 Title: RELION: implementation of a Bayesian approach to cryo-EM structure determination. Authors: Scheres SH | |||||||||
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_11221.map.gz | 67.8 MB | EMDB map data format | |
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Header (meta data) | emd-11221-v30.xml emd-11221.xml | 41.1 KB 41.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11221_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_11221.png | 246 KB | ||
Masks | emd_11221_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-11221.cif.gz | 8.2 KB | ||
Others | emd_11221_additional_1.map.gz emd_11221_additional_2.map.gz emd_11221_additional_3.map.gz emd_11221_half_map_1.map.gz emd_11221_half_map_2.map.gz | 80.5 MB 96.5 MB 10.3 MB 80.9 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11221 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11221 | HTTPS FTP |
-Validation report
Summary document | emd_11221_validation.pdf.gz | 887.2 KB | Display | EMDB validaton report |
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Full document | emd_11221_full_validation.pdf.gz | 886.8 KB | Display | |
Data in XML | emd_11221_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_11221_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11221 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11221 | HTTPS FTP |
-Related structure data
Related structure data | 6zhyMC 6zhxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10465 (Title: Single-particle cryo-EM dataset of the complex between a nucleosome and the regulatory linker of ALC1 Data size: 6.8 TB Data #1: Unaligned movies of the nucleosome - ALC1-linker complex - session_1_disk_1 [micrographs - multiframe] Data #2: Unaligned movies of the nucleosome - ALC1-linker complex - session_1_disk_2 [micrographs - multiframe] Data #3: Unaligned movies of the nucleosome - ALC1-linker complex - session_1_disk_3 [micrographs - multiframe] Data #4: Unaligned movies of the nucleosome - ALC1-linker complex - session_2_grid_1 [micrographs - multiframe] Data #5: Unaligned movies of the nucleosome - ALC1-linker complex - session_2_grid_2 [micrographs - multiframe] Data #6: Particles of the high-resolution nucleosome class [picked particles - multiframe - processed] Data #7: Particles of the hexasome class [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11221.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map filtered by local resolution from RELION LocalRes procedure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.654 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_11221_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map from final 3D refinement in RELION.
File | emd_11221_additional_1.map | ||||||||||||
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Annotation | Map from final 3D refinement in RELION. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map from RELION PostProcess.
File | emd_11221_additional_2.map | ||||||||||||
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Annotation | Map from RELION PostProcess. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map from RELION PostProcess with masking.
File | emd_11221_additional_3.map | ||||||||||||
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Annotation | Map from RELION PostProcess with masking. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1 from final 3D refinement in RELION.
File | emd_11221_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 from final 3D refinement in RELION. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1 from final 3D refinement in RELION.
File | emd_11221_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 from final 3D refinement in RELION. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : A hexasome (nucleosome lacking one of the two H2A-H2B dimers) wit...
+Supramolecule #1: A hexasome (nucleosome lacking one of the two H2A-H2B dimers) wit...
+Supramolecule #2: Histones
+Supramolecule #3: DNA
+Supramolecule #4: Chromodomain-helicase-DNA-binding protein 1-like
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Chromodomain-helicase-DNA-binding protein 1-like
+Macromolecule #5: DNA (110-MER) Widom 601 sequence
+Macromolecule #6: DNA (110-MER) Widom 601 sequence
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: current 20 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 19897 / Average electron dose: 50.4 e/Å2 Details: Movies were collected in counting mode. Total exposure was fractionated over 60 movie frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Real-space CC between model and map | ||||||||||||||||||||
Output model | PDB-6zhy: |