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- EMDB-4692: Human-D02 Nucleosome Core Particle with biotin-streptavidin label -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4692 | |||||||||
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Title | Human-D02 Nucleosome Core Particle with biotin-streptavidin label | |||||||||
![]() | human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | |||||||||
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![]() | chromatin / nucleosome / retrovirus / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / subtelomeric heterochromatin formation ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / subtelomeric heterochromatin formation / single fertilization / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / male gonad development / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / enzyme binding / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Wilson MD / Nans A / Pye VE / Cherepanov P / 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. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.8 KB 29.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 56.8 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() ![]() | 59.8 MB 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 361.3 KB | Display | ![]() |
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Full document | ![]() | 360.4 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r0cMC ![]() 4693C ![]() 4960C ![]() 6rnyC M: atomic model generated by this map C: citing same article ( |
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Similar 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 | human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 map for human nucleosome core particle wrapped...
File | emd_4692_additional.map | ||||||||||||
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Annotation | unmasked map for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1 for human nucleosome core particle...
File | emd_4692_half_map_1.map | ||||||||||||
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Annotation | half map 1 for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1 for human nucleosome core particle...
File | emd_4692_half_map_2.map | ||||||||||||
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Annotation | half map 1 for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human-D02 Nucleosome Core Particle with biotin-streptavidin label
+Supramolecule #1: Human-D02 Nucleosome Core Particle with biotin-streptavidin label
+Supramolecule #2: Histones
+Supramolecule #3: DNA
+Macromolecule #1: Histone H3.3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B type 1-C/E/F/G/I
+Macromolecule #5: DNA (142-MER)
+Macromolecule #6: DNA (142-MER)
+Macromolecule #7: MANGANESE (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.176 mg/mL | |||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Streptavidin incubated D02-biotin nucleosomes were crosslinked with glutaraldehye. This was quenched and the sample spin concentrated |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4182 / Average exposure time: 60.0 sec. / Average electron dose: 28.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix. |
Refinement | Space: REAL |
Output model | ![]() PDB-6r0c: |