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- PDB-6qi5: Near Atomic Structure of an Atadenovirus Shows a possible gene du... -
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Basic information
Entry | Database: PDB / ID: 6qi5 | ||||||
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Title | Near Atomic Structure of an Atadenovirus Shows a possible gene duplication event and Intergenera Variations in Cementing Proteins | ||||||
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![]() | VIRUS / adenovirus atadenovirus virus evolution | ||||||
Function / homology | ![]() hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / endocytosis involved in viral entry into host cell / viral capsid / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Condezo, G.N. / Marabini, R. / Gomez-Blanco, J. / SanMartin, C. | ||||||
![]() | ![]() 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: ![]() Title: Near Atomic Structure of an Atadenovirus Reveals a Conserved Capsid-Binding Motif and Intergenera Variations in Cementing Proteins Authors: Marabini, R. / Condezo, G.N. / Gomez-Blanco, J. / San Martin, C. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4551MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 101861.930 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 41158.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 30744.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 67049.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 50619.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Lizard adenovirus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 150 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Heloderma horridum |
Virus shell | Diameter: 940 nm / Triangulation number (T number): 25 |
Buffer solution | pH: 7.4 / Details: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid type: Quantifoil R2/4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 2 sec. / Electron dose: 54 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16071 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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