PDBsum entry 1x9p

Virus like particle

PDB id: 1x9p

Contents

Protein chain

460 a.a. *

Ligands

SO4

C15 ×2

* Residue conservation analysis

PDB id:

1x9p

Name:

Virus like particle

Title:

The crystal structure of human adenovirus 2 penton base

Structure:

Penton protein. Chain: a. Fragment: residues 49-571. Synonym: virion component iii, penton base protein. Engineered: yes

Source:

Human adenovirus 2. Organism_taxid: 10515. Gene: penton base. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five.

Resolution:

3.30Å R-factor: 0.307 R-free: 0.307

Authors:

C.Zubieta,G.Schoehn,J.Chroboczek,S.Cusack

Key ref:

C.Zubieta et al. (2005). The structure of the human adenovirus 2 penton. Mol Cell, 17, 121-135. PubMed id: 15629723 DOI: 10.1016/j.molcel.2004.11.041

Date:

24-Aug-04 Release date: 18-Jan-05

Protein chain

P03276  (CAPSP_ADE02) -  Penton protein from Human adenovirus C serotype 2

Seq: 571 a.a.

Struc: 460 a.a.

DOI no: 10.1016/j.molcel.2004.11.041

Mol Cell 17:121-135 (2005)

PubMed id: 15629723

The structure of the human adenovirus 2 penton.

C.Zubieta, G.Schoehn, J.Chroboczek, S.Cusack.

ABSTRACT

The adenovirus penton, a noncovalent complex of the pentameric penton base and trimeric fiber proteins, comprises the vertices of the adenovirus capsid and contains all necessary components for viral attachment and internalization. The 3.3 A resolution crystal structure of human adenovirus 2 (hAd2) penton base shows that the monomer has a basal jellyroll domain and a distal irregular domain formed by two long insertions, a similar topology to the adenovirus hexon. The Arg-Gly-Asp (RGD) motif, required for interactions with cellular integrins, occurs on a flexible surface loop. The complex of penton base with bound N-terminal fiber peptide, determined at 3.5 A resolution, shows that the universal fiber motif FNPVYPY binds at the interface of adjacent penton base monomers and results in a localized structural rearrangement in the insertion domain of the penton base. These results give insight into the structure and assembly of the adenovirus capsid and will be of use for gene-therapy applications.

Selected figure(s)

Figure 3.
Figure 3. Structure of the Adenovirus 2 Penton Base(A) Left, tricolor ribbon representation of the monomer with the jellyroll domain (green) and the insertion domain (blue, residues 129–434; red, residues 466–519). The termini are labeled N and C. The variable loop and the RGD loop are labeled with disordered residues 298–373 of the RGD loop depicted by a dotted line. Putative zwittergent 3-12 molecules are drawn as stick representations. Right, rainbow ribbon representation colored from N terminus (blue) to C terminus (red) viewed after rotation of approximately 90° from previous image.(B) Stereo view of the putative zwittergent 3-12 binding site on the penton base monomer. The detergent molecules are colored green. Interacting residues from the protein are cyan.(C) The pentamer, the functional unit of the penton base protein, shown as a surface representation (left) and ribbon diagram (right), with each monomer colored uniquely. The variable loop, RGD loop and N- and C termini are marked.

Figure 4.
Figure 4. Fiber Peptide Interactions with the Penton Base(A) Stereo diagram of the fiber peptide (red) bound to the penton base subunit interface viewed looking down the 5-fold axis.(B) Stereo view of the peptide binding site. The ribbon diagrams of the monomers are colored blue and green and the bound peptide is depicted as sticks with carbons colored white. Residues forming the peptide binding pocket are colored yellow for monomer A and orange for monomer B. Putative hydrogen bonding interactions are denoted by dashed yellow lines.(C) Stereo view of the experimental averaged electron density of the bound peptide.(D) Sequence alignment of the N-terminal portion of representative fiber proteins from serotypes Ad2, accession number P03275; Ad3, P04501; Ad7, AAR89975; Ad11, NP_852715; Ad12, DAA00575; Ad17, DAA00599; Ad25, NP_478420; Ad37, AAB71734; Ad41 short fiber, P16883; and Ad41 long fiber, P14267. Conserved residues (yellow) and the peptide sequence used for structural analysis (red) are highlighted.

The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 17, 121-135) copyright 2005.

Figures were selected by an automated process.