6SIT

Pseudo-atomic crystal structure of the desmoglein 2 - human adenovirus serotype 3 fibre knob complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.367 

wwPDB Validation 3D Report Full Report


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Literature

Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2.

Vassal-Stermann, E.Hutin, S.Fender, P.Burmeister, W.P.

(2019) Acta Crystallogr.,Sect.F 75: 750-757

  • DOI: 10.1107/S2053230X19015784

  • PubMed Abstract: 
  • The cryo-electron microscopy (cryo-EM) structure of the complex between the trimeric human adenovirus B serotype 3 fibre knob and human desmoglein 2 fragments containing cadherin domains EC2 and EC3 has been published, showing 3:1 and 3:2 complexes. ...

    The cryo-electron microscopy (cryo-EM) structure of the complex between the trimeric human adenovirus B serotype 3 fibre knob and human desmoglein 2 fragments containing cadherin domains EC2 and EC3 has been published, showing 3:1 and 3:2 complexes. Here, the crystal structure determined at 4.5 Å resolution is presented with one EC2-EC3 desmoglein fragment bound per fibre knob monomer in the asymmetric unit, leading to an apparent 3:3 stoichiometry. However, in concentrated solution the 3:2 complex is predominant, as shown by small-angle X-ray scattering (SAXS), while cryo-EM at lower concentrations showed a majority of the 3:1 complex. Substitution of the calcium ions bound to the desmoglein domains by terbium ions allowed confirmation of the X-ray model using their anomalous scattering and shows that at least one binding site per cluster of calcium ions is intact and exchangeable and, combined with SAXS data, that the cadherin domains are folded even in the distal part that is invisible in the cryo-EM reconstruction.


    Organizational Affiliation

    Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38000 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fiber protein
A
191Human adenovirus B serotype 3Mutation(s): 0 
Find proteins for P04501 (Human adenovirus B serotype 3)
Go to UniProtKB:  P04501
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Desmoglein-2
D
238Homo sapiensMutation(s): 0 
Gene Names: DSG2 (CDHF5)
Find proteins for Q14126 (Homo sapiens)
Go to Gene View: DSG2
Go to UniProtKB:  Q14126
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.367 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 146.530α = 90.00
b = 146.530β = 90.00
c = 146.530γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-02
French National Research AgencyFranceANR-10-LABX-49-01

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release