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- EMDB-4960: PFV intasome - nucleosome strand transfer complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4960
TitlePFV intasome - nucleosome strand transfer complex
Map data
SampleNucleosome core particle bound by PFV intasome post in the post catalytic state:
Nucleosome / (Integrase) x 2 / Human DNA / DNA / Histone H3.3H3F3A / Histone H4 / Histone H2A type 1 / Histone H2B type 1-C/E/F/G/I / (nucleic-acidNucleic acid) x 5 / ligand
Function / homology
Function and homology information


negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin assembly / subtelomeric heterochromatin assembly / nucleus organization / nucleosomal DNA binding / spermatid development / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin assembly / subtelomeric heterochromatin assembly / nucleus organization / nucleosomal DNA binding / spermatid development / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / negative regulation of megakaryocyte differentiation / depurination / positive regulation of histone exchange / Packaging Of Telomere Ends / oogenesis / CENP-A containing chromatin assembly / negative regulation of DNA recombination at telomere / single fertilization / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / telomere capping / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Inhibition of DNA recombination at telomere / RNA polymerase II core promoter sequence-specific DNA binding / Meiotic synapsis / heterochromatin assembly => GO:0031507 / embryo implantation / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / DNA replication-dependent chromatin assembly / DNA methylation / HCMV Late Events / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / rDNA heterochromatin assembly / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / negative regulation of gene expression, epigenetic / PRC2 methylates histones and DNA / mitotic chromosome condensation / regulation of gene silencing by miRNA / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Formation of the beta-catenin:TCF transactivating complex / regulation of megakaryocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / Metalloprotease DUBs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / nucleosome assembly / RMTs methylate histone arginines / HCMV Early Events / regulation of androgen receptor signaling pathway / Pre-NOTCH Transcription and Translation / osteoblast differentiation / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / virion component => GO:0044423 / UCH proteinases / Transcriptional regulation of granulopoiesis / male gonad development / cell population proliferation / E3 ubiquitin ligases ubiquitinate target proteins / viral genome integration into host DNA / viral penetration into host nucleus / RNA-directed DNA polymerase / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RNA-directed DNA polymerase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA integration / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / double-strand break repair via nonhomologous end joining / double-strand break repair / Processing of DNA double-strand break ends / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / viral life cycle / chromosome, telomeric region / positive regulation of cell growth / Oxidative Stress Induced Senescence / antibacterial humoral response
Similarity search - Function
Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / Histone H2B signature. ...Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / RNase H / Integrase core domain / Integrase catalytic domain profile. / Integrase, catalytic core / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Histone H2A type 1 / Pro-Pol polyprotein / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human) / Human spumaretrovirus / Pyrobaculum filamentous virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsRenault L / Maskell DP / Wilson MD / Cherepanov P / Costa A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC0010061 United Kingdom
The Francis Crick InstituteFC0010065 United Kingdom
CitationJournal: 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
DepositionMay 9, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rny
  • Surface level: 0.07
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4960.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 266.64 Å
1.11 Å/pix.
x 240 pix.
= 266.64 Å
1.11 Å/pix.
x 240 pix.
= 266.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.111 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.33225438 - 0.65916705
Average (Standard dev.)0.0013075157 (±0.014830548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 266.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1111.1111.111
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z266.640266.640266.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.3320.6590.001

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Supplemental data

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Half map: Half map 1 of Nucleosome core particle bound...

Fileemd_4960_half_map_1.map
AnnotationHalf map 1 of Nucleosome core particle bound by PFV intasome post catalytic state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1 of Nucleosome core particle bound...

Fileemd_4960_half_map_2.map
AnnotationHalf map 1 of Nucleosome core particle bound by PFV intasome post catalytic state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Nucleosome core particle bound by PFV intasome post in the post c...

EntireName: Nucleosome core particle bound by PFV intasome post in the post catalytic state
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
Number of Components: 16

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Component #1: protein, Nucleosome core particle bound by PFV intasome post in t...

ProteinName: Nucleosome core particle bound by PFV intasome post in the post catalytic state
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
Recombinant expression: No
MassTheoretical: 399 kDa

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Component #2: protein, Nucleosome

ProteinName: Nucleosome / Details: Nucleosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Integrase

ProteinName: Integrase / Details: Integrase / Recombinant expression: No
SourceSpecies: Human spumaretrovirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Human DNA

ProteinName: Human DNA / Details: Human DNA / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: synthetic construct (others)

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Component #5: protein, DNA

ProteinName: DNA / Details: DNA / Recombinant expression: No
SourceSpecies: Pyrobaculum filamentous virus 1
Source (engineered)Expression System: synthetic construct (others)

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Component #6: protein, Histone H3.3

ProteinName: Histone H3.3H3F3A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.360983 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.121537 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Histone H2B type 1-C/E/F/G/I

ProteinName: Histone H2B type 1-C/E/F/G/I / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.937213 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, Integrase

ProteinName: Integrase / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 44.456695 kDa
SourceSpecies: Human spumaretrovirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: nucleic-acid, DNA (128-MER)

nucleic acidName: DNA (128-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DA)(DC)(DA)(DC)(DT)(DA)(DC) (DC)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DG)(DA) (DA)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT)(DC) (DA)(DC)(DC)(DA)(DG)(DC) ...Sequence:
(DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DA)(DC)(DA)(DC)(DT)(DA)(DC) (DC)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DG)(DA) (DA)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT)(DC) (DA)(DC)(DC)(DA)(DG)(DC)(DC)(DA)(DG)(DG) (DC)(DC)(DT)(DT)(DG)(DA)(DA)(DT)(DG)(DC) (DA)(DA)(DT)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DT)(DA)(DG)(DG)(DA)(DA)(DT)(DA)(DT) (DT)(DT)(DG)(DG)(DA)(DC)(DT)(DT)(DC)(DC) (DC)(DC)(DA)(DC)(DC)(DT)(DA)(DC)(DC)(DA) (DT)(DT)(DC)(DA)(DG)(DG)(DT)(DA)(DA)(DC) (DT)(DT)(DG)(DA)(DT)(DA)(DC)(DA)(DA)(DA) (DC)(DA)(DC)(DA)(DG)(DC)(DC)(DC)
MassTheoretical: 39.189094 kDa
SourceSpecies: Homo sapiens (human)

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Component #12: nucleic-acid, DNA (108-MER)

nucleic acidName: DNA (108-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DG)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT) (DT)(DG)(DT)(DA)(DT)(DC)(DA)(DA)(DG)(DT) (DT)(DA)(DC)(DC)(DT)(DG)(DA)(DA)(DT)(DG) (DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(DG) (DA)(DA)(DG)(DT)(DC)(DC) ...Sequence:
(DG)(DG)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT) (DT)(DG)(DT)(DA)(DT)(DC)(DA)(DA)(DG)(DT) (DT)(DA)(DC)(DC)(DT)(DG)(DA)(DA)(DT)(DG) (DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(DG) (DA)(DA)(DG)(DT)(DC)(DC)(DA)(DA)(DA)(DT) (DA)(DT)(DT)(DC)(DC)(DT)(DA)(DG)(DT)(DA) (DA)(DG)(DA)(DC)(DA)(DA)(DT)(DT)(DG)(DC) (DA)(DT)(DT)(DC)(DA)(DA)(DG)(DG)(DC)(DC) (DT)(DG)(DG)(DC)(DT)(DG)(DG)(DT)(DG)(DA) (DA)(DA)(DC)(DC)(DT)(DG)(DT)(DT)(DT)(DC) (DC)(DT)(DG)(DG)(DG)(DA)(DA)(DG)
MassTheoretical: 33.581453 kDa
SourceSpecies: Homo sapiens (human)

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Component #13: nucleic-acid, DNA (33-MER)

nucleic acidName: DNA (33-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DT)(DC) (DT)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG)(DT) (DG)(DA)(DA)(DA)(DA)(DC)(DC)(DA)(DA)(DC) (DT)(DA)(DA)
MassTheoretical: 10.114523 kDa
SourceSpecies: Homo sapiens (human)

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Component #14: nucleic-acid, DNA (53-MER)

nucleic acidName: DNA (53-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DA)(DC)(DA)(DG)(DT)(DA)(DG) (DT)(DT)(DA)(DG)(DT)(DT)(DG)(DG)(DT)(DT) (DT)(DT)(DC)(DA)(DC)(DC)(DA)(DC)(DA)(DG) (DG)(DG)(DA)(DG)(DA)(DA) ...Sequence:
(DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DA)(DC)(DA)(DG)(DT)(DA)(DG) (DT)(DT)(DA)(DG)(DT)(DT)(DG)(DG)(DT)(DT) (DT)(DT)(DC)(DA)(DC)(DC)(DA)(DC)(DA)(DG) (DG)(DG)(DA)(DG)(DA)(DA)(DC)(DC)(DT)(DG) (DG)(DA)(DC)
MassTheoretical: 16.397531 kDa
SourceSpecies: Homo sapiens (human)

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Component #15: nucleic-acid, DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*T...

nucleic acidName: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DT)(DG)(DT)(DC)(DA)(DT)(DG)(DG) (DA)(DA)(DT)(DT)(DT)(DC)(DG)(DC)(DA)
MassTheoretical: 5.834794 kDa
SourceSpecies: Pyrobaculum filamentous virus 1

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Component #16: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/mL / pH: 7
VitrificationInstrument: LEICA EM CPC / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 80 % / Details: 1 min incubation 3.5s blot.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 56 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1.5 - 3.5 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 4916

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 177155
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.9 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
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. ...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.
Input PDB model: 3UTB, 3OS0
Output model

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