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- EMDB-51372: Human Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex at... -

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Basic information

Entry
Database: EMDB / ID: EMD-51372
TitleHuman Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex at 3.6A resolution.
Map dataRDAd5_FX_virion_3p6A
Sample
  • Complex: Human Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex
KeywordsHuman Adenovirus 5 Hexon Coagulation Factors FX / VIRUS
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 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 16, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51372.png

Downloads & links

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Map

FileDownload / File: emd_51372.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRDAd5_FX_virion_3p6A
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: 0.007
Minimum - Maximum-0.026811643 - 0.064344525
Average (Standard dev.)0.001244795 (±0.0047888253)
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: RDAd5 FX virion 3p6A

Fileemd_51372_half_map_1.map
AnnotationRDAd5_FX_virion_3p6A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RDAd5 FX virion 3p6A

Fileemd_51372_half_map_2.map
AnnotationRDAd5_FX_virion_3p6A
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) and Coagulation Factor X (FX) complex

EntireName: Human Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex
Components
  • Complex: Human Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex

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Supramolecule #1: Human Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex

SupramoleculeName: Human Adenovirus 5 (Ad5) and Coagulation Factor X (FX) complex
type: complex / ID: 1 / Parent: 0 / Details: Icosahedral (I1) reconstruction
Source (natural)Organism: Human adenovirus 5
Molecular weightTheoretical: 150 MDa

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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. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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: 10000 / 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 59391
Details: Manual picking followed by reference based auto-picking
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6b1t

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 26000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6b1t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation

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