1X9T

The crystal structure of human adenovirus 2 penton base in complex with an ad2 N-terminal fibre peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.306 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

The structure of the human adenovirus 2 penton

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

(2005) Mol Cell 17: 121-135

  • DOI: https://doi.org/10.1016/j.molcel.2004.11.041
  • Primary Citation of Related Structures:  
    1X9P, 1X9T

  • PubMed 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.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble Cedex 9, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penton protein523Human adenovirus 2Mutation(s): 0 
Gene Names: penton base
UniProt
Find proteins for P03276 (Human adenovirus C serotype 2)
Explore P03276 
Go to UniProtKB:  P03276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03276
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal peptide of Fiber protein21N/AMutation(s): 0 
UniProt
Find proteins for P03275 (Human adenovirus C serotype 2)
Explore P03275 
Go to UniProtKB:  P03275
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03275
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C15
Query on C15

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
C17 H38 N O3 S
IZWSFJTYBVKZNK-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.306 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 438.37α = 90
b = 299.825β = 103.22
c = 419.583γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
RAVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description