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- EMDB-4551: Near Atomic Structure of an Atadenovirus Shows a possible gene du... -

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Basic information

Entry
Database: EMDB / ID: EMD-4551
TitleNear Atomic Structure of an Atadenovirus Shows a possible gene duplication event and Intergenera Variations in Cementing Proteins
Map data
SampleLizard adenovirus 2:
virus / Hexon protein / Protein LH3 / Pre-hexon-linking protein VIII / PIIIa / Penton protein
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / endocytosis involved in viral entry into host cell / viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / nucleus
Adenovirus large t-antigen, E1B 55kDa protein / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, N-terminal / Pectin lyase fold/virulence factor / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Adenovirus penton base protein / in:ipr016111: / Group II dsDNA virus coat/capsid protein
Penton protein / Pre-hexon-linking protein VIII / Protein LH3 / PIIIa / Hexon protein
Biological speciesLizard adenovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCondezo GN / Marabini R / Gomez-Blanco J / SanMartin C
Citation
Journal: Sci Adv / Year: 2021
Title: Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins.
Authors: Roberto Marabini / Gabriela N Condezo / Mart Krupovic / Rosa Menéndez-Conejero / Josué Gómez-Blanco / Carmen San Martín /
Abstract: Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with ...Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with nonmammalian host: lizard atadenovirus LAdV-2. We find a large conformational difference in the internal vertex protein IIIa between mast- and atadenoviruses, induced by the presence of an extended polypeptide. This polypeptide, and α-helical clusters beneath the facet, likely correspond to genus-specific proteins LH2 and p32k. Another genus-specific protein, LH3, with a fold typical of bacteriophage tailspikes, contacts the capsid surface via a triskelion structure identical to that used by mastadenovirus protein IX, revealing a conserved capsid-binding motif and an ancient gene duplication event. Our data also suggest that mastadenovirus E1B-55 K was exapted from the atadenovirus-like LH3 protein. This work provides new information on the evolution of adenoviruses, emphasizing the importance of minor coat proteins for determining specific physicochemical properties of virions and most likely their tropism.
#1: Journal: Biorxiv / Year: 2020
Title: Near Atomic Structure of an Atadenovirus Reveals a Conserved Capsid-Binding Motif and Intergenera Variations in Cementing Proteins
Authors: Marabini R / Condezo GN / Gomez-Blanco J / San Martin C
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJan 17, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseAug 5, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qi5
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qi5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4551.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 780 pix.
= 1053. Å
1.35 Å/pix.
x 780 pix.
= 1053. Å
1.35 Å/pix.
x 780 pix.
= 1053. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.05
Minimum - Maximum-0.2957798 - 0.5360727
Average (Standard dev.)0.0033348403 (±0.038650833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-390-390-390
Dimensions780780780
Spacing780780780
CellA=B=C: 1053.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z780780780
origin x/y/z0.0000.0000.000
length x/y/z1053.0001053.0001053.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS-390-390-390
NC/NR/NS780780780
D min/max/mean-0.2960.5360.003

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Supplemental data

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Sample components

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Entire Lizard adenovirus 2

EntireName: Lizard adenovirus 2 / Number of components: 6

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Component #1: virus, Lizard adenovirus 2

VirusName: Lizard adenovirus 2 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 150 MDa
SpeciesSpecies: Lizard adenovirus 2
Source (natural)Host Species: Heloderma horridum (Mexican beaded lizard)

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Component #2: protein, Hexon protein

ProteinName: Hexon protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 101.86193 kDa
SourceSpecies: Lizard adenovirus 2

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Component #3: protein, Protein LH3

ProteinName: Protein LH3 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 41.158344 kDa
SourceSpecies: Lizard adenovirus 2

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Component #4: protein, Pre-hexon-linking protein VIII

ProteinName: Pre-hexon-linking protein VIII / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 30.744453 kDa
SourceSpecies: Lizard adenovirus 2

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Component #5: protein, PIIIa

ProteinName: PIIIa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.049266 kDa
SourceSpecies: Lizard adenovirus 2

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Component #6: protein, Penton protein

ProteinName: Penton protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.619848 kDa
SourceSpecies: Lizard adenovirus 2

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: PBS / pH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 54 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 16071
3D reconstructionSoftware: RELION, Scipion / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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