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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 dataNucleosome 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
Function / homology
Function and homology information


nucleosomal DNA binding / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine ...nucleosomal DNA binding / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / 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 / 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 / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / virion component / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / DNA integration / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / UCH proteinases / RNA-directed DNA polymerase activity / nucleosome / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / antimicrobial humoral immune response mediated by antimicrobial peptide / RNA-DNA hybrid ribonuclease activity / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / host cell cytoplasm / chromosome, telomeric region / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / Ub-specific processing proteases / defense response to Gram-positive bacterium / symbiont entry into host cell / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / host cell nucleus / enzyme binding / protein-containing complex / proteolysis / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding
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 / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / 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 / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / 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 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Histone-fold / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like 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
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  • Surface view with fitted model
  • Atomic models: PDB-6rny
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4960.png

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)
AnnotationNucleosome core particle bound by PFV intasome post catalytic state
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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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
Components
  • Complex: Nucleosome core particle bound by PFV intasome post in the post catalytic state
    • Complex: Nucleosome
      • Protein or peptide: Histone H3.3H3F3A
      • 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...

SupramoleculeName: 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
Molecular weightTheoretical: 399 KDa

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Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: Nucleosome
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Integrase

SupramoleculeName: Integrase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5 / Details: Integrase
Source (natural)Organism: Human spumaretrovirus
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Human DNA

SupramoleculeName: Human DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#9 / Details: Human DNA
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #5: DNA

SupramoleculeName: DNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #10 / Details: DNA
Source (natural)Organism: Pyrobaculum filamentous virus 1
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.360983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.121537 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.937213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

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Macromolecule #5: Integrase

MacromoleculeName: Integrase / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Human spumaretrovirus
Molecular weightTheoretical: 44.456695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGCNTKKPN LDAELDQLLQ GHYIKGYPKQ YTYFLEDGKV KVSRPEGVKI IPPQSDRQKI VLQAHNLAHT GREATLLKIA NLYWWPNMR KDVVKQLGRC QQCLITNASN KASGPILRPD RPQKPFDKFF IDYIGPLPPS QGYLYVLVVV DGMTGFTWLY P TKAPSTSA ...String:
GPGCNTKKPN LDAELDQLLQ GHYIKGYPKQ YTYFLEDGKV KVSRPEGVKI IPPQSDRQKI VLQAHNLAHT GREATLLKIA NLYWWPNMR KDVVKQLGRC QQCLITNASN KASGPILRPD RPQKPFDKFF IDYIGPLPPS QGYLYVLVVV DGMTGFTWLY P TKAPSTSA TVKSLNVLTS IAIPKVIHSD QGAAFTSSTF AEWAKERGIH LEFSTPYHPQ SSGKVERKNS DIKRLLTKLL VG RPTKWYD LLPVVQLALN NTYSPVLKYT PHQLLFGIDS NTPFANQDTL DLTREEELSL LQEIRTSLYH PSTPPASSRS WSP VVGQLV QERVARPASL RPRWHKPSTV LKVLNPRTVV ILDHLGNNRT VSIDNLKPTS HQNGTTNDTA TMDHLEKNE

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Macromolecule #6: DNA (128-MER)

MacromoleculeName: DNA (128-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.189094 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #7: DNA (108-MER)

MacromoleculeName: DNA (108-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.581453 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #8: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.114523 KDa
SequenceString:
(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)

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Macromolecule #9: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.397531 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #10: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')

MacromoleculeName: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')
type: dna / ID: 10 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Pyrobaculum filamentous virus 1
Molecular weightTheoretical: 5.834794 KDa
SequenceString:
(DA)(DT)(DT)(DG)(DT)(DC)(DA)(DT)(DG)(DG) (DA)(DA)(DT)(DT)(DT)(DC)(DG)(DC)(DA)

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7 / Component - Concentration: 1.0 MM / Component - Name: DTT
GridModel: C-flat-1/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen 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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 59000
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (NeCEN netherlands)
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3125
CTF correctionSoftware - Name: CTFFIND (ver. 1.4)
Startup modelType of model: OTHER
Details: initial model based EMDB-2992 low pass filtered to 50A
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber 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.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
Final reconstructionNumber 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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

3utb

,

3os0

)
DetailsThe 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.
RefinementSpace: REAL
Output model

PDB-6rny:
PFV intasome - nucleosome strand transfer complex

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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