- EMDB-4960: PFV intasome - nucleosome strand transfer complex -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-4960
Title
PFV intasome - nucleosome strand transfer complex
Map data
Nucleosome core particle bound by PFV intasome post catalytic state
Sample
Complex: Nucleosome core particle bound by PFV intasome post in the post catalytic state
Complex: Nucleosome
Protein or peptide: x 4 types
Complex: Integrase
Protein or peptide: x 1 types
Complex: Human DNA
DNA: x 4 types
Complex: DNA
DNA: x 1 types
Ligand: x 1 types
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 / 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 / virion component / 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 / DNA integration / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / viral genome integration into host DNA / Transcriptional regulation of granulopoiesis / osteoblast differentiation / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / male gonad development / RNA-directed DNA polymerase activity / nucleosome / host cell / RNA-DNA hybrid ribonuclease activity / nucleosome assembly / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / DNA recombination / Estrogen-dependent gene expression / cell population proliferation / host cell cytoplasm / chromosome, telomeric region / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity Similarity search - Function
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
Deposition
May 9, 2019
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Header (metadata) release
Sep 25, 2019
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Map release
Sep 25, 2019
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Update
May 22, 2024
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Current status
May 22, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Nucleosome core particle bound by PFV intasome post in the post c...
Entire
Name: Nucleosome core particle bound by PFV intasome post in the post catalytic state
Components
Complex: Nucleosome core particle bound by PFV intasome post in the post catalytic state
Complex: Nucleosome
Protein or peptide: Histone H3.3
Protein or peptide: Histone H4
Protein or peptide: Histone H2A type 1
Protein or peptide: Histone H2B type 1-C/E/F/G/I
Complex: Integrase
Protein or peptide: Integrase
Complex: Human DNA
DNA: DNA (128-MER)
DNA: DNA (108-MER)
DNA: DNA (33-MER)
DNA: DNA (53-MER)
Complex: DNA
DNA: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')
Ligand: MAGNESIUM ION
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Supramolecule #1: Nucleosome core particle bound by PFV intasome post in the post c...
Supramolecule
Name: Nucleosome core particle bound by PFV intasome post in the post catalytic state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 Details: human histones refolded as an octamer with native human D02 sequence. PFV intasome formed form short annealed oligos and PFV integrase. complex formed by mixing and separated by SEC. ...Details: human histones refolded as an octamer with native human D02 sequence. PFV intasome formed form short annealed oligos and PFV integrase. complex formed by mixing and separated by SEC. Catalysis initiated by addition of Magnesium ions
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.
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Electron microscopy
Microscope
FEI TITAN KRIOS
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
Type of model: OTHER Details: initial model based EMDB-2992 low pass filtered to 50A
Final reconstruction
Number classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 177155
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
Final 3D classification
Number classes: 4 / Avg.num./class: 59000 / Software - Name: RELION (ver. 1.3) Details: Two rounds of 3D classification. First with 8 classes coarse sampling, second with 4 classes.
source_name: PDB, initial_model_type: experimental model
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: PFV intasome - nucleosome strand transfer complex
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