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- EMDB-15694: Human adenovirus type 5 lacking core protein V -

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Basic information

Entry
Database: EMDB / ID: EMD-15694
TitleHuman adenovirus type 5 lacking core protein V
Map dataHuman adenovirus type 5 lacking core protein V
Sample
  • Virus: Ad5 deltaV (virus)
KeywordsHAdV-C5 / deltaV / VIRUS
Biological speciesAd5 deltaV (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHernando-Perez M / San Martin C / Martin-Gonzalez N / Gomez-Gonzalez A / Bauer M / Greber UF / de Pablo PJ
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2019-104098GB-I00/AEI/10.13039/501100011033 Spain
CitationJournal: Sci Adv / Year: 2023
Title: Adenovirus core protein V reinforces the capsid and enhances genome release from disrupted particles.
Authors: Natalia Martín-González / Alfonso Gómez-González / Mercedes Hernando-Pérez / Michael Bauer / Urs F Greber / Carmen San Martín / Pedro J de Pablo /
Abstract: Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro ...Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro disassembly of particles lacking protein V (Ad5-ΔV). Ad5-ΔV particles were softer and less brittle than the wild-type ones (Ad5-wt), but they were more prone to release pentons under mechanical fatigue. In Ad5-ΔV, core components did not readily diffuse out of partially disrupted capsids, and the core appeared more condensed than in Ad5-wt. These observations suggest that instead of condensing the genome, protein V antagonizes the condensing action of the other core proteins. Protein V provides mechanical reinforcement and facilitates genome release by keeping DNA connected to capsid fragments that detach during disruption. This scenario is in line with the location of protein V in the virion and its role in Ad5 cell entry.
History
DepositionAug 30, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15694.png

Downloads & links

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Map

FileDownload / File: emd_15694.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman adenovirus type 5 lacking core protein V
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 640 pix.
= 1296. Å		2.03 Å/pix.
x 640 pix.
= 1296. Å		2.03 Å/pix.
x 640 pix.
= 1296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0152
Minimum - Maximum-0.023639265 - 0.04693445
Average (Standard dev.)-0.0010316152 (±0.0058323042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 1296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half2 map in the same coordinate space as the primary map

Fileemd_15694_half_map_1.map
AnnotationHalf2 map in the same coordinate space as the primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half1 map in the same coordinate space as the primary map

Fileemd_15694_half_map_2.map
AnnotationHalf1 map in the same coordinate space as the primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ad5 deltaV

EntireName: Ad5 deltaV (virus)
Components
  • Virus: Ad5 deltaV (virus)

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Supramolecule #1: Ad5 deltaV

SupramoleculeName: Ad5 deltaV / type: virus / ID: 1 / Parent: 0
Details: Deletion mutant described in https://doi.org/10.1126/sciadv.abl7150
NCBI-ID: 129951 / Sci species name: Ad5 deltaV / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
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

BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Cloride
10.0 mMNa2HPO4Sodium phosphate dibasic
2.7 mMKClPotasium Cloride
1.8 mMKH2PO4Potassium phosphate monobasic
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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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: 1-50 / Number grids imaged: 1 / Number real images: 2106 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.442 µm / Calibrated defocus min: 0.483 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: 8151
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 6550
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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