+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4299 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Class 3 : translocated nucleosome | |||||||||
Map data | Class 3 : Translocated nucleosome | |||||||||
Sample |
| |||||||||
Keywords | nucleosome / cryo EM / nucleosome sliding / chromatin remodeling / GENE REGULATION | |||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Synthetic construct (others) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Bilokapic S / Halic M | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural rearrangements of the histone octamer translocate DNA. Authors: Silvija Bilokapic / Mike Strauss / Mario Halic / Abstract: Nucleosomes, the basic unit of chromatin, package and regulate expression of eukaryotic genomes. Nucleosomes are highly dynamic and are remodeled with the help of ATP-dependent remodeling factors. ...Nucleosomes, the basic unit of chromatin, package and regulate expression of eukaryotic genomes. Nucleosomes are highly dynamic and are remodeled with the help of ATP-dependent remodeling factors. Yet, the mechanism of DNA translocation around the histone octamer is poorly understood. In this study, we present several nucleosome structures showing histone proteins and DNA in different organizational states. We observe that the histone octamer undergoes conformational changes that distort the overall nucleosome structure. As such, rearrangements in the histone core α-helices and DNA induce strain that distorts and moves DNA at SHL 2. Distortion of the nucleosome structure detaches histone α-helices from the DNA, leading to their rearrangement and DNA translocation. Biochemical assays show that cross-linked histone octamers are immobilized on DNA, indicating that structural changes in the octamer move DNA. This intrinsic plasticity of the nucleosome is exploited by chromatin remodelers and might be used by other chromatin machineries. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4299.map.gz | 11.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4299-v30.xml emd-4299.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_4299.png | 165.6 KB | ||
Filedesc metadata | emd-4299.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4299 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4299 | HTTPS FTP |
-Validation report
Summary document | emd_4299_validation.pdf.gz | 221.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4299_full_validation.pdf.gz | 221 KB | Display | |
Data in XML | emd_4299_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4299 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4299 | HTTPS FTP |
-Related structure data
Related structure data | 6fq8MC 4297C 4298C 6fq5C 6fq6C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4299.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Class 3 : Translocated nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Class 1 : Canonical nucleosome
Entire | Name: Class 1 : Canonical nucleosome |
---|---|
Components |
|
-Supramolecule #1: Class 1 : Canonical nucleosome
Supramolecule | Name: Class 1 : Canonical nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Molecular weight | Theoretical: 200 KDa |
-Supramolecule #2: Class 1 : Canonical nucleosome
Supramolecule | Name: Class 1 : Canonical nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Supramolecule #3: Class 1 : Canonical nucleosome
Supramolecule | Name: Class 1 : Canonical nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 |
---|---|
Source (natural) | Organism: Synthetic construct (others) |
-Macromolecule #1: Histone H3.3C
Macromolecule | Name: Histone H3.3C / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 11.560538 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVALFED TNLCAIHAKR VTIMPKDIQ LARRIRGER UniProtKB: Histone H3.3C |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 9.86159 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 12.082128 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KTRAKAKTRS SRAGLQFPVG RVHRLLRKGN YAERVGAGAP VYLAAVLEYL TAEILELAGN AARDNKKTRI IPRHLQLAVR NDEELNKLL GRVTIAQGGV LPNIQSVLLP K UniProtKB: Histone H2A |
-Macromolecule #4: Histone H2B
Macromolecule | Name: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 10.635226 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAV TKYTSA UniProtKB: Histone H2B |
-Macromolecule #5: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.604047 KDa |
Sequence | String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG) |
-Macromolecule #6: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.145754 KDa |
Sequence | String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 39000 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |