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- EMDB-46615: Human adenovirus 5 (Ad5) in complex with coagulation Factor II (P... -

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Basic information

Entry
Database: EMDB / ID: EMD-46615
TitleHuman adenovirus 5 (Ad5) in complex with coagulation Factor II (Prothrombin) at 4.13 resolution.
Map dataRDAd5_FII_virion_4.13A
Sample
  • Complex: Human adenovirus 5 (Ad5) in complex with coagulation Factor II (Prothrombin)
KeywordsHuman adenovirus 5 Hexon Blood Coagulation Factors II Binding Complex / VIRUS
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.13 Å
AuthorsReddy VS / Ma OX
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161367 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure-derived insights from blood factors binding to the surfaces of different adenoviruses.
Authors: Haley E Mudrick / Shao-Chia Lu / Janarjan Bhandari / Mary E Barry / Jack R Hemsath / Felix G M Andres / Olivia X Ma / Michael A Barry / Vijay S Reddy /
Abstract: The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of ...The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of several human adenoviruses with human platelet factor-4 (PF4), coagulation factors FII (Prothrombin), and FX. While we observed EM densities for FII and FX bound to all the species-C adenoviruses examined, no densities were seen for PF4, even though PF4 can co-pellet with various Ads. Similar to FX, the γ-carboxyglutamic acid (Gla) domain of FII binds within the surface cavity of hexon trimers. While FII binds equally to species-C Ads: Ad5, Ad6, and Ad657, FX exhibits significantly better binding to Ad5 and Ad657 compared to Ad6. Although only the FX-Gla domain is observed at high-resolution (3.7 Å), the entire FX is visible at low-resolution bound to Ad5 in three equivalent binding modes consistent with the 3-fold symmetric hexon. Only the Gla and kringle-1 domains of FII are visible on all the species-C adenoviruses, where the rigid FII binds in an upright fashion, in contrast to the flexible and bent FX. These data suggest that differential binding of FII and FX may shield certain species-C adenoviruses differently against immune molecules, thereby modulating their tropism.
History
DepositionAug 17, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46615.png

Downloads & links

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Map

FileDownload / File: emd_46615.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRDAd5_FII_virion_4.13A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 400 pix.
= 563.2 Å		1.41 Å/pix.
x 800 pix.
= 1126.4 Å		1.41 Å/pix.
x 800 pix.
= 1126.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.04237034 - 0.07732111
Average (Standard dev.)0.0016220144 (±0.0064111436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00400
Dimensions800800400
Spacing800800400
CellA: 1126.4 Å / B: 1126.4 Å / C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46615_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46615_half_map_2.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 : Human adenovirus 5 (Ad5) in complex with coagulation Factor II (P...

EntireName: Human adenovirus 5 (Ad5) in complex with coagulation Factor II (Prothrombin)
Components
  • Complex: Human adenovirus 5 (Ad5) in complex with coagulation Factor II (Prothrombin)

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Supramolecule #1: Human adenovirus 5 (Ad5) in complex with coagulation Factor II (P...

SupramoleculeName: Human adenovirus 5 (Ad5) in complex with coagulation Factor II (Prothrombin)
type: complex / ID: 1 / Parent: 0 / Details: Icosahedral (I1) reconstruction
Source (natural)Organism: Human adenovirus 5

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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

Concentration2 mg/mL
BufferpH: 7.2
Details: 50mM HEPES pH 7.2, 300mM NaCl, 10mM CaCl2 and 5mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K
DetailsHuman adenovirus in complex with coagulation Factor II (Prothrombin)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 2 / Number real images: 7842 / Average exposure time: 5.0 sec. / Average electron dose: 80.0 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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12842
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6b1t

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 2324
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation Coefficient

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