2C4I

Crystal structure of engineered avidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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


Literature

Controlling Quaternary Structure Assembly: Subunit Interface Engineering and Crystal Structure of Dual Chain Avidin.

Hytonen, V.P.Horha, J.Airenne, T.T.Niskanen, E.A.Helttunen, K.Johnson, M.S.Salminen, T.A.Kulomaa, M.S.Nordlund, H.R.

(2006) J Mol Biol 359: 1352

  • DOI: https://doi.org/10.1016/j.jmb.2006.04.044
  • Primary Citation of Related Structures:  
    2C4I

  • PubMed Abstract: 

    Dual chain avidin (dcAvd) is an engineered avidin form, in which two circularly permuted chicken avidin monomers are fused into one polypeptide chain. DcAvd can theoretically form two different pseudotetrameric quaternary assemblies because of symmetry at the monomer-monomer interfaces. Here, our aim was to control the assembly of the quaternary structure of dcAvd. We introduced the mutation I117C into one of the circularly permuted domains of dcAvd and scanned residues along the 1-3 subunit interface of the other domain. Interestingly, V115H resulted in a single, disulfide locked quaternary assembly of dcAvd, whereas I117H could not guide the oligomerisation process even though it stabilised the protein. The modified dcAvd forms were found to retain their characteristic pseudotetrameric state both at high and low pH, and were shown to bind D-biotin at levels comparable to that of wild-type chicken avidin. The crystal structure of dcAvd-biotin complex at 1.95 Angstroms resolution demonstrates the formation of the functional dcAvd pseudotetramer at the atomic level and reveals the molecular basis for its special properties. Altogether, our data facilitate further engineering of the biotechnologically valuable dcAvd scaffold and gives insights into how to guide the quaternary structure assembly of oligomeric proteins.


  • Organizational Affiliation

    NanoScience Center, Department of Biological and Environmental Science, University of Jyväskylä, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AVIDIN271Gallus gallusMutation(s): 0 
UniProt
Find proteins for P02701 (Gallus gallus)
Explore P02701 
Go to UniProtKB:  P02701
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02701
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.037α = 90
b = 79.037β = 90
c = 84.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description