4AQQ

Dodecahedron formed of penton base protein from adenovirus Ad3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.75 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structural Basis for the Integrity of Adenovirus Ad3 Dodecahedron.

Szolajska, E.Burmeister, W.P.Zochowska, M.Nerlo, B.Andreev, I.Schoehn, G.Andrieu, J.P.Fender, P.Naskalska, A.Zubieta, C.Cusack, S.Chroboczek, J.

(2012) PLoS One 7: 46075

  • DOI: 10.1371/journal.pone.0046075
  • Primary Citation of Related Structures:  
    4AQQ, 4AR2

  • PubMed Abstract: 
  • During the viral life cycle adenoviruses produce excess capsid proteins. Human adenovirus serotype 3 (Ad3) synthesizes predominantly an excess of free pentons, the complexes of pentameric penton base and trimeric fiber proteins, which are responsible for virus penetration ...

    During the viral life cycle adenoviruses produce excess capsid proteins. Human adenovirus serotype 3 (Ad3) synthesizes predominantly an excess of free pentons, the complexes of pentameric penton base and trimeric fiber proteins, which are responsible for virus penetration. In infected cells Ad3 pentons spontaneously assemble into dodecahedral virus-like nano-particles containing twelve pentons. They also form in insect cells during expression in the baculovirus system. Similarly, in the absence of fiber protein dodecahedric particles built of 12 penton base pentamers can be produced. Both kinds of dodecahedra show remarkable efficiency of intracellular penetration and can be engineered to deliver several millions of foreign cargo molecules to a single target cell. For this reason, they are of great interest as a delivery vector. In order to successfully manipulate this potential vector for drug and/or gene delivery, an understanding of the molecular basis of vector assembly and integrity is critical. Crystallographic data in conjunction with site-directed mutagenesis and biochemical analysis provide a model for the molecular determinants of dodecamer particle assembly and the requirements for stability. The 3.8 Å crystal structure of Ad3 penton base dodecamer (Dd) shows that the dodecahedric structure is stabilized by strand-swapping between neighboring penton base molecules. Such N-terminal strand-swapping does not occur for Dd of Ad2, a serotype which does not form Dd under physiological conditions. This unique stabilization of the Ad3 dodecamer is controlled by residues 59-61 located at the site of strand switching, the residues involved in putative salt bridges between pentamers and by the disordered N-terminus (residues 1-47), as confirmed by site directed mutagenesis and biochemical analysis of mutant and wild type protein. We also provide evidence that the distal N-terminal residues are externally exposed and available for attaching cargo.


    Organizational Affiliation

    Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland. ewasz@ibb.waw.pl



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L2 PROTEIN III (PENTON BASE)A509Human adenovirus B3Mutation(s): 0 
Gene Names: L2
UniProt
Find proteins for Q2Y0H9 (Human adenovirus B serotype 3)
Explore Q2Y0H9 
Go to UniProtKB:  Q2Y0H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2Y0H9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.75 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.291 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 342.701α = 90
b = 342.701β = 90
c = 342.701γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation