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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4693 | |||||||||
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Title | Structure of a human nucleosome at 3.5 A resolution | |||||||||
![]() | Masked Structure of a human nucleosome wrapped with 171bp of Widom-601 strong positioning DNA at 3.5 A resolution. | |||||||||
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Function / homology | ![]() negative regulation of chromosome condensation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wilson MD / Nans A / Costa A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer. Authors: Marcus D Wilson / Ludovic Renault / Daniel P Maskell / Mohamed Ghoneim / Valerie E Pye / Andrea Nans / David S Rueda / Peter Cherepanov / Alessandro Costa / ![]() ![]() Abstract: Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase ...Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers. #1: ![]() Title: Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamerDNA looping and sliding along the histone octamer Authors: Wilson MD / Renault L / Makell DP / Ghoneim M / Pye VE / Cherepanov P / Nans A / Rueda D / Cherepanov P / Costa A | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.2 KB 23.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 71.7 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 59.9 MB 59.9 MB 48.5 MB 48.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Masked Structure of a human nucleosome wrapped with 171bp of Widom-601 strong positioning DNA at 3.5 A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unmasked Structure of a human nucleosome wrapped with...
File | emd_4693_additional.map | ||||||||||||
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Annotation | Unmasked Structure of a human nucleosome wrapped with 171bp of Widom-601 strong positioning DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unmasked Structure of a human nucleosome wrapped with...
File | emd_4693_additional_1.map | ||||||||||||
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Annotation | Unmasked Structure of a human nucleosome wrapped with 171bp of Widom-601 strong positioning DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2 from relion-2.1b refinement of human...
File | emd_4693_half_map_1.map | ||||||||||||
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Annotation | half map 2 from relion-2.1b refinement of human nucleosome wrapped with 171bp of Widom-601 strong positioning DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1 from relion-2.1b refinement of human...
File | emd_4693_half_map_2.map | ||||||||||||
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Annotation | half map 1 from relion-2.1b refinement of human nucleosome wrapped with 171bp of Widom-601 strong positioning DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : human nucleosome particle
Entire | Name: human nucleosome particle |
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Components |
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-Supramolecule #1: human nucleosome particle
Supramolecule | Name: human nucleosome particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: recombinant human nucleosmes generated by expression of individual human histones and PCR synthesis of 171bp Widonm 601 DNA |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 215 KDa |
-Supramolecule #2: octamer of human histones
Supramolecule | Name: octamer of human histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: recombinantly expressed human histones, H2A.1, H2B, H3.1, H4 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Supramolecule #3: 171bp widom-601 DNA
Supramolecule | Name: 171bp widom-601 DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 / Details: widom-601 DNA generated by PCR |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.180 mg/mL | ||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00039 kPa / Details: 40mA on EMS glowdischarge unit | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blotforce -1 blottime 4s. | ||||||||
Details | quantified based on DNA absorbtion at A260 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | grids screened manully and loaded into krios, optimal grid selected for |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1300 / Average exposure time: 60.0 sec. / Average electron dose: 31.3 e/Å2 / Details: Falcon III counting mode 30 frames |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Protocol: RIGID BODY FIT |