1H0T

An affibody in complex with a target protein: structure and coupled folding


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 40 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND GOOD RAMACHANDRAN PLOTS 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An Affibody in Complex with a Target Protein: Structure and Coupled Folding

Wahlberg, E.Lendel, C.Helgstrand, M.Allard, P.Dincbas-Renqvist, V.Hedqvist, A.Berglund, H.Nygren, P.-A.Hard, T.

(2003) Proc Natl Acad Sci U S A 100: 3185-3190

  • DOI: https://doi.org/10.1073/pnas.0436086100
  • Primary Citation of Related Structures:  
    1H0T

  • PubMed Abstract: 

    Combinatorial protein engineering provides powerful means for functional selection of novel binding proteins. One class of engineered binding proteins, denoted affibodies, is based on the three-helix scaffold of the Z domain derived from staphylococcal protein A. The Z(SPA-1) affibody has been selected from a phage-displayed library as a binder to protein A. Z(SPA-1) also binds with micromolar affinity to its own ancestor, the Z domain. We have characterized the Z(SPA-1) affibody in its uncomplexed state and determined the solution structure of a Z:Z(SPA-1) protein-protein complex. Uncomplexed Z(SPA-1) behaves as an aggregation-prone molten globule, but folding occurs on binding, and the original (Z) three-helix bundle scaffold is fully formed in the complex. The structural basis for selection and strong binding is a large interaction interface with tight steric and polar/nonpolar complementarity that directly involves 10 of 13 mutated amino acid residues on Z(SPA-1). We also note similarities in how the surface of the Z domain responds by induced fit to binding of Z(SPA-1) and Ig Fc, respectively, suggesting that the Z(SPA-1) affibody is capable of mimicking the morphology of the natural binding partner for the Z domain.


  • Organizational Affiliation

    Department of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN G BINDING PROTEIN A58Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P02976 
Go to UniProtKB:  P02976
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02976
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ZSPA-1 AFFIBODY58synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 40 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND GOOD RAMACHANDRAN PLOTS 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-27
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Derived calculations, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Other