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- EMDB-4448: Adenovirus major core protein condenses DNA in clusters and bundl... -

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Basic information

Entry
Database: EMDB / ID: EMD-4448
TitleAdenovirus major core protein condenses DNA in clusters and bundles, modulating genome release and capsid internal pressure.
Map dataHuman Adenovirus type 5 Ad5/attP vector with deletions in the E1 and E3 regions and an attP insertion flanking psi and a GFP cassette following psi.
Sample
  • Virus: Ad5/attP (virus)
Biological speciesAd5/attP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.54 Å
AuthorsHernando-Perez M / San Martin M / Condezo GN / Hearing P
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU-2016-74868-P Spain
CitationJournal: Nucleic Acids Res / Year: 2019
Title: Adenovirus major core protein condenses DNA in clusters and bundles, modulating genome release and capsid internal pressure.
Authors: Natalia Martín-González / Mercedes Hernando-Pérez / Gabriela N Condezo / Marta Pérez-Illana / Antonio Šiber / David Reguera / Philomena Ostapchuk / Patrick Hearing / Carmen San Martín ...Authors: Natalia Martín-González / Mercedes Hernando-Pérez / Gabriela N Condezo / Marta Pérez-Illana / Antonio Šiber / David Reguera / Philomena Ostapchuk / Patrick Hearing / Carmen San Martín / Pedro J de Pablo /
Abstract: Some viruses package dsDNA together with large amounts of positively charged proteins, thought to help condense the genome inside the capsid with no evidence. Further, this role is not clear because ...Some viruses package dsDNA together with large amounts of positively charged proteins, thought to help condense the genome inside the capsid with no evidence. Further, this role is not clear because these viruses have typically lower packing fractions than viruses encapsidating naked dsDNA. In addition, it has recently been shown that the major adenovirus condensing protein (polypeptide VII) is dispensable for genome encapsidation. Here, we study the morphology and mechanics of adenovirus particles with (Ad5-wt) and without (Ad5-VII-) protein VII. Ad5-VII- particles are stiffer than Ad5-wt, but DNA-counterions revert this difference, indicating that VII screens repulsive DNA-DNA interactions. Consequently, its absence results in increased internal pressure. The core is slightly more ordered in the absence of VII and diffuses faster out of Ad5-VII- than Ad5-wt fractured particles. In Ad5-wt unpacked cores, dsDNA associates in bundles interspersed with VII-DNA clusters. These results indicate that protein VII condenses the adenovirus genome by combining direct clustering and promotion of bridging by other core proteins. This condensation modulates the virion internal pressure and DNA release from disrupted particles, which could be crucial to keep the genome protected inside the semi-disrupted capsid while traveling to the nuclear pore.
History
DepositionNov 30, 2018-
Header (metadata) releaseDec 19, 2018-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4448.png

Downloads & links

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Map

FileDownload / File: emd_4448.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Adenovirus type 5 Ad5/attP vector with deletions in the E1 and E3 regions and an attP insertion flanking psi and a GFP cassette following psi.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 752 pix.
= 1030.24 Å		1.37 Å/pix.
x 752 pix.
= 1030.24 Å		1.37 Å/pix.
x 752 pix.
= 1030.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.041537672 - 0.08872718
Average (Standard dev.)0.0040665427 (±0.016050514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions752752752
Spacing752752752
CellA=B=C: 1030.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z752752752
origin x/y/z0.0000.0000.000
length x/y/z1030.2401030.2401030.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ224224224
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS752752752
D min/max/mean-0.0420.0890.004

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Supplemental data

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Sample components

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Entire : Ad5/attP

EntireName: Ad5/attP (virus)
Components
  • Virus: Ad5/attP (virus)

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Supramolecule #1: Ad5/attP

SupramoleculeName: Ad5/attP / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 129951 / Sci species name: Ad5/attP / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK293
Molecular weightTheoretical: 150 MDa
Virus shellShell ID: 1 / Diameter: 950.0 Å / T number (triangulation number): 25

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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

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Cloride
10.0 mMNa2HPO4Sodium phosphate dibasic
2.7 mMKClPotasium Cloride
1.8 mMKH2PO4Potassium phosphate monobasic
GridModel: Quantifoil R2/4 / Material: COPPER/RHODIUM
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC
Details0.2 mg/ml initial specimen concentration was increased by consecutively incubating the grid on 10 drops of specimen before the final blotting and plunging in liquid ethane.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-31 / Number grids imaged: 1 / Number real images: 4395 / Average exposure time: 1.65 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.115 µm / Calibrated defocus min: 0.374 µm / Calibrated magnification: 73000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 26661
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 23060
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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