+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4960 | |||||||||
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Title | PFV intasome - nucleosome strand transfer complex | |||||||||
Map data | Nucleosome core particle bound by PFV intasome post catalytic state | |||||||||
Sample |
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Keywords | chromatin / nucleosome / retrovirus / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / nucleus organization ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / nucleus organization / spermatid development / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / single fertilization / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / RNA polymerase II core promoter sequence-specific DNA binding / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / embryo implantation / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / 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 / multicellular organism growth / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / osteoblast differentiation / viral penetration into host nucleus / structural constituent of chromatin / male gonad development / UCH proteinases / RNA-directed DNA polymerase activity / nucleosome / host cell / antimicrobial humoral immune response mediated by antimicrobial peptide / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / HATs acetylate histones / antibacterial humoral response / chromosome, telomeric region / aspartic-type endopeptidase activity / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / cell population proliferation / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human spumaretrovirus / Pyrobaculum filamentous virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Renault L / Maskell DP / Wilson MD / Cherepanov P / Costa A | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2019 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4960.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-4960-v30.xml emd-4960.xml | 34.2 KB 34.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4960_fsc.xml | 7.7 KB | Display | FSC data file |
Images | emd_4960.png | 281.4 KB | ||
Filedesc metadata | emd-4960.cif.gz | 8.4 KB | ||
Others | emd_4960_half_map_1.map.gz emd_4960_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4960 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4960 | HTTPS FTP |
-Validation report
Summary document | emd_4960_validation.pdf.gz | 646.6 KB | Display | EMDB validaton report |
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Full document | emd_4960_full_validation.pdf.gz | 646.2 KB | Display | |
Data in XML | emd_4960_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | emd_4960_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4960 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4960 | HTTPS FTP |
-Related structure data
Related structure data | 6rnyMC 4692C 4693C 6r0cC C: citing same article (ref.) M: atomic model generated by this map |
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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_4960.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Nucleosome core particle bound by PFV intasome post catalytic state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.111 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 1 of Nucleosome core particle bound...
File | emd_4960_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of Nucleosome core particle bound...
File | emd_4960_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Nucleosome core particle bound by PFV intasome post in the post c...
+Supramolecule #1: Nucleosome core particle bound by PFV intasome post in the post c...
+Supramolecule #2: Nucleosome
+Supramolecule #3: Integrase
+Supramolecule #4: Human DNA
+Supramolecule #5: 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: Integrase
+Macromolecule #6: DNA (128-MER)
+Macromolecule #7: DNA (108-MER)
+Macromolecule #8: DNA (33-MER)
+Macromolecule #9: DNA (53-MER)
+Macromolecule #10: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')
+Macromolecule #11: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7 / Component - Concentration: 1.0 MM / Component - Name: DTT |
Grid | Model: C-flat-1/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM CPC / Details: 1 min incubation 3.5s blot. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Microscope was modified with a Cs corrector (NeCEN netherlands) |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 4916 / Average exposure time: 1.6 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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: 59000 |
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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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 and namdinator. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix. | ||||||
Refinement | Space: REAL | ||||||
Output model | PDB-6rny: |