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- EMDB-3821: Cryo-EM reconstruction of a modified human Adenovirus C5 -

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Basic information

Entry
Database: EMDB / ID: EMD-3821
TitleCryo-EM reconstruction of a modified human Adenovirus C5
Map data
Sample
  • Virus: Human adenovirus 5
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsSchmid M / Ernst P / Honegger A / Suomalainen M / Zimmermann M / Braun L / Stauffer S / Thom C / Dreier B / Eibauer M ...Schmid M / Ernst P / Honegger A / Suomalainen M / Zimmermann M / Braun L / Stauffer S / Thom C / Dreier B / Eibauer M / Kipar A / Vogel V / Greber UF / Medalia O / Plueckthun A
CitationJournal: Nat Commun / Year: 2018
Title: Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control.
Authors: Markus Schmid / Patrick Ernst / Annemarie Honegger / Maarit Suomalainen / Martina Zimmermann / Lukas Braun / Sarah Stauffer / Cristian Thom / Birgit Dreier / Matthias Eibauer / Anja Kipar / ...Authors: Markus Schmid / Patrick Ernst / Annemarie Honegger / Maarit Suomalainen / Martina Zimmermann / Lukas Braun / Sarah Stauffer / Cristian Thom / Birgit Dreier / Matthias Eibauer / Anja Kipar / Viola Vogel / Urs F Greber / Ohad Medalia / Andreas Plückthun /
Abstract: Most systemic viral gene therapies have been limited by sequestration and degradation of virions, innate and adaptive immunity, and silencing of therapeutic genes within the target cells. Here we ...Most systemic viral gene therapies have been limited by sequestration and degradation of virions, innate and adaptive immunity, and silencing of therapeutic genes within the target cells. Here we engineer a high-affinity protein coat, shielding the most commonly used vector in clinical gene therapy, human adenovirus type 5. Using electron microscopy and crystallography we demonstrate a massive coverage of the virion surface through the hexon-shielding scFv fragment, trimerized to exploit the hexon symmetry and gain avidity. The shield reduces virion clearance in the liver. When the shielded particles are equipped with adaptor proteins, the virions deliver their payload genes into human cancer cells expressing HER2 or EGFR. The combination of shield and adapter also increases viral gene delivery to xenografted tumors in vivo, reduces liver off-targeting and immune neutralization. Our study highlights the power of protein engineering for viral vectors overcoming the challenges of local and systemic viral gene therapies.
History
DepositionJul 21, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseFeb 7, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6eqc
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6eqc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3821.png

Downloads & links

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Map

FileDownload / File: emd_3821.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 800 pix.
= 1568. Å		1.96 Å/pix.
x 800 pix.
= 1568. Å		1.96 Å/pix.
x 800 pix.
= 1568. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.01913177 - 0.079589896
Average (Standard dev.)0.002493746 (±0.00791669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1568.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.961.961.96
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z1568.0001568.0001568.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.0190.0800.002

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Supplemental data

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Half map: #1

Fileemd_3821_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_3821_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

EntireName: Human adenovirus 5
Components
  • Virus: Human adenovirus 5

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 0.4 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0.17)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4cwu
PDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 1880
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6eqc:
Cryo-EM reconstruction of a complex of a binding protein and human adenovirus C5 hexon

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