EMDB-1178: Structure of the dodecahedral penton particle from human adenovir...

Basic information

• Entry: Database: EMDB / ID: EMD-1178
• Title: Structure of the dodecahedral penton particle from human adenovirus type 3.
• Map data: The pixel size has been calibrated using the X-ray structure of adenovirus 2 penton base. Accession number 1X9P

Sample

• Sample: adenovirus 3 penton base dodecahedron
• Protein or peptide: Ad3 penton base

Function / homology

Function:

T=25 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral capsid / clathrin-dependent endocytosis of virus by host cell / cell adhesion / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell

Domain/homology:

Adenovirus penton base protein / Adenovirus penton base protein / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain

Component:

Fiber protein / Penton protein / L5 fiber

• Biological species: Human adenovirus 3
• Method: single particle reconstruction / cryo EM / negative staining / Resolution: 9.3 Å
• Authors: Fuschiotti P / Schoehn G / Fender P / Fabry CMS / Hewat EA / Chroboczek J
• Citation: Journal: J Mol Biol / Year: 2006; Title: Structure of the dodecahedral penton particle from human adenovirus type 3.; Authors: P Fuschiotti / G Schoehn / P Fender / C M S Fabry / E A Hewat / J Chroboczek / R W H Ruigrok / J F Conway / ; Abstract: The sub-viral dodecahedral particle of human adenovirus type 3, composed of the viral penton base and fiber proteins, shares an important characteristic of the entire virus: it can attach to cells and penetrate them. Structure determination of the fiberless dodecahedron by cryo-electron microscopy to 9 Angstroms resolution reveals tightly bound pentamer subunits, with only minimal interfaces between penton bases stabilizing the fragile dodecahedron. The internal cavity of the dodecahedron is approximately 80 Angstroms in diameter, and the interior surface is accessible to solvent through perforations of approximately 20 Angstroms diameter between the pentamer towers. We observe weak density beneath pentamers that we attribute to a penton base peptide including residues 38-48. The intact amino-terminal domain appears to interfere with pentamer-pentamer interactions and its absence by mutation or proteolysis is essential for dodecamer assembly. Differences between the 9 Angstroms dodecahedron structure and the adenovirus serotype 2 (Ad2) crystallographic model correlate closely with differences in sequence. The 3D structure of the dodecahedron including fibers at 16 Angstroms resolution reveals extra density on the top of the penton base that can be attributed to the fiber N terminus. The fiber itself exhibits striations that correlate with features of the atomic structure of the partial Ad2 fiber and that represent a repeat motif present in the amino acid sequence. These new observations offer important insights into particle assembly and stability, as well as the practicality of using the dodecahedron in targeted drug delivery. The structural work provides a sound basis for manipulating the properties of this particle and thereby enhancing its value for such therapeutic use.

History

Deposition	Nov 4, 2005	-
Header (metadata) release	Nov 4, 2005	-
Map release	Nov 7, 2005	-
Update	Oct 24, 2012	-
Current status	Oct 24, 2012	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_1178.map.gz / Format: CCP4 / Size: 40.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
• Annotation: The pixel size has been calibrated using the X-ray structure of adenovirus 2 penton base. Accession number 1X9P
• Voxel size: X=Y=Z: 1.37 Å

Density

Contour Level	By AUTHOR: 91.900000000000006 / Movie #1: 110
Minimum - Maximum	-335.0 - 509.0
Average (Standard dev.)	3.05461431 (±52.415409089999997)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -139 -139 -139 Dimensions 279 279 279 Spacing 279 279 279
Cell	A=B=C: 382.23 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Integer*27
Å/pix. X/Y/Z	1.37	1.37	1.37
M x/y/z	279	279	279
origin x/y/z	0.000	0.000	0.000
length x/y/z	382.230	382.230	382.230
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	-77	-77	0
NX/NY/NZ	155	155	78
MAP C/R/S	1	2	3
start NC/NR/NS	-139	-139	-139
NC/NR/NS	279	279	279
D min/max/mean	-335.000	509.000	3.055

Supplemental data

Sample components

Entire : adenovirus 3 penton base dodecahedron

• Entire: Name: adenovirus 3 penton base dodecahedron

Components

• Sample: adenovirus 3 penton base dodecahedron
• Protein or peptide: Ad3 penton base

Supramolecule #1000: adenovirus 3 penton base dodecahedron

• Supramolecule: Name: adenovirus 3 penton base dodecahedron / type: sample / ID: 1000 ; Details: The penton base was expressed in baculovirus abd the penton base self-assemble into dodecahedrons; Oligomeric state: 12 pentamers / Number unique components: 1
• Molecular weight: Experimental: 3.5 MDa

Macromolecule #1: Ad3 penton base

• Macromolecule: Name: Ad3 penton base / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Oligomeric state: dodecamer of pentamer / Recombinant expression: Yes
• Source (natural): Organism: Human adenovirus 3 / synonym: human adenovirus 3
• Molecular weight: Experimental: 60 KDa / Theoretical: 60 KDa
• Recombinant expression: Organism: unidentified baculovirus / Recombinant plasmid: pAcUW31

Experimental details

Structure determination

• Method: negative staining, cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 1 mg/mL
• Buffer: pH: 6.6 / Details: 25 mM phosphate buffer at pH 6.6
• Staining: Type: NEGATIVE; Details: Quantifoil R2 1 grids (Quantifoil Micro Tools GmbH, Germany) were loaded with 4 ul of sample at 1 mg ml, blotted and rapidly frozen in liquid ethane within a liquid nitrogen bath using a Zeiss cryoplunger
• Grid: Details: Quantifoil R2/1 grids
• Vitrification: Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Zeiss cryoplunger

Electron microscopy

• Microscope: JEOL 2010F
• Electron beam: Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Calibrated magnification: 51100 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
• Sample stage: Specimen holder: Eucentric / Specimen holder model: OTHER
• Temperature: Average: 100 K
• Alignment procedure: Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000
• Image recording: Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 14

Image processing

• CTF correction: Details: each negative or each focal pair
• Final reconstruction: Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT EM3DR PFT2 EM3DR2 / Number images used: 1849
• Details: The particles were selected using X3d