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- EMDB-11109: Locally reconstructed HAdV-F41 penton base -

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Basic information

Entry
Database: EMDB / ID: EMD-11109
TitleLocally reconstructed HAdV-F41 penton base
Map dataFull Map
Sample
  • Virus: Human adenovirus 41
Biological speciesHuman adenovirus 41
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsCarlson L-A / Rafie K
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)CDA00047/2017-C Sweden
Swedish Research CouncilDnr 2017-00859 Sweden
Swedish Research CouncilDnr 2019-01472 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Sci Adv / Year: 2021
Title: The structure of enteric human adenovirus 41-A leading cause of diarrhea in children.
Authors: K Rafie / A Lenman / J Fuchs / A Rajan / N Arnberg / L-A Carlson /
Abstract: Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and ...Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present the first structure of an enteric HAdV-HAdV-F41-determined by cryo-electron microscopy to a resolution of 3.8 Å. The structure reveals extensive alterations to the virion exterior as compared to nonenteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of core protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation of enteric HAdVs to a fundamentally different tissue tropism.
History
DepositionMay 31, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11109.png

Downloads & links

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Map

FileDownload / File: emd_11109.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 250 pix.
= 260.25 Å		1.04 Å/pix.
x 250 pix.
= 260.25 Å		1.04 Å/pix.
x 250 pix.
= 260.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.03137083 - 0.040441956
Average (Standard dev.)-0.0003332862 (±0.0035349373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 260.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z260.250260.250260.250
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0310.040-0.000

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Supplemental data

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Mask #1

Fileemd_11109_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_11109_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_11109_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human adenovirus 41

EntireName: Human adenovirus 41
Components
  • Virus: Human adenovirus 41

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Supramolecule #1: Human adenovirus 41

SupramoleculeName: Human adenovirus 41 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 / NCBI-ID: 10524 / Sci species name: Human adenovirus 41 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 900.0 Å

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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

Concentration4.2 mg/mL
BufferpH: 7.4
Details: PBS buffer made from comemrcial PBS tablets Medicargo, PBS tablets, 09-9400-100
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-20 / Number grids imaged: 2 / Number real images: 6929 / Average electron dose: 1.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1168320
CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: EMDB MAP
EMDB ID:

7034

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta) / Software - details: Run through Scipion / Number images used: 412038
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta) / Software - details: Run through Scipion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta) / Software - details: Run through Scipion
Final 3D classificationSoftware - Name: RELION (ver. 3.0-beta) / Software - details: Run through Scipion

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Atomic model buiding 1

Initial modelPDB ID:

6z7n


Chain - Chain ID: M
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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