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- EMDB-53655: Human Adenovirus D 10 Fiber Shaft by Focussed Refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-53655
TitleHuman Adenovirus D 10 Fiber Shaft by Focussed Refinement
Map dataRELION postprocess sharpened map of half map 1 and half map 2.
Sample
  • Virus: Human adenovirus D10
Keywordsadenovirus / fiber / viral receptor / knob / VIRUS
Biological speciesHuman adenovirus D10
Methodsingle particle reconstruction / cryo EM / Resolution: 4.61 Å
AuthorsWaraich K / Mundy RM / Bates EA / da Fonseca P / Morris E / Rizkallah PJ / Baker AT / T Young M / Parker AL / Bhella D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Citation
Journal: PLoS Pathog / Year: 2026
Title: Identification of a novel fiber shaft structural motif and overexpression of key transcripts elucidated in human adenovirus D 10.
Authors: Rosie M Mundy / Kasim Waraich / Emily A Bates / Pierre J Rizkallah / Alexander T Baker / Mark T Young / Edward Morris / Paula C A da Fonseca / Carly M Bliss / David Matthews / David Bhella / Alan L Parker /
Abstract: Adenoviruses are widely used as vectors for subunit vaccines and oncolytic therapies. Efficient vectors must infect target cells and deliver therapeutic transgenes at high levels. Species D ...Adenoviruses are widely used as vectors for subunit vaccines and oncolytic therapies. Efficient vectors must infect target cells and deliver therapeutic transgenes at high levels. Species D adenoviruses, such as human adenovirus type 10 (HAdV-D10), are promising candidates due to low seroprevalence in humans. Here, we present the cryo-electron microscopy structure of the HAdV-D10 capsid alongside transcriptomic profiling of infected cells to inform vector development. The fiber shaft, essential for cell entry, was resolved at 10 Å, revealing a previously uncharacterized 'umbrella' motif. Viral transcript analysis using an ORF-centric pipeline uncovered key differences from HAdV-C5, including abundant expression of a transcript encoding a protein equivalent to mature protein VII. These findings highlight the importance of detailed vector characterization prior to clinical translation and support the advancement of HAdV-D10 as a next-generation platform for gene delivery and vaccine development.
#1: Journal: Biorxiv / Year: 2025
Title: Identification of a novel structural motif and overexpression of key transcripts elucidated in Adenovirus 10
Authors: Mundy RM / Waraich K / Bates EA / Rizkallah PJ / Baker AT / Young MT / Morris E / da Fonseca PCA / Bliss CM / Matthews D / Bhella D / Parker AL
History
DepositionMay 12, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53655.png

Downloads & links

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Map

FileDownload / File: emd_53655.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION postprocess sharpened map of half map 1 and half map 2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 200 pix.
= 331.6 Å		1.66 Å/pix.
x 200 pix.
= 331.6 Å		1.66 Å/pix.
x 200 pix.
= 331.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0132
Minimum - Maximum-0.04251457 - 0.0740801
Average (Standard dev.)-0.0009305195 (±0.005439276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 331.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53655_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of local refinement of adenovirus fiber shaft.

Fileemd_53655_half_map_1.map
AnnotationHalf map 2 of local refinement of adenovirus fiber shaft.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of local refinement of adenovirus fiber shaft.

Fileemd_53655_half_map_2.map
AnnotationHalf map 1 of local refinement of adenovirus fiber shaft.
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 D10

EntireName: Human adenovirus D10
Components
  • Virus: Human adenovirus D10

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Supramolecule #1: Human adenovirus D10

SupramoleculeName: Human adenovirus D10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 28275 / Sci species name: Human adenovirus D10 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)

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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 / Details: Phosphate Buffered Saline (PBS)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5524
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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