1ZDB

PHAGE-SELECTED MINI PROTEIN A DOMAIN, Z38, NMR, MINIMIZED MEAN STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 56 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST RESTRAINT VIOLATION ENERGY 

wwPDB Validation   3D Report Full Report

Currently 1ZDB does not have a validation slider image.


This is version 1.3 of the entry. See complete history


Literature

Structural mimicry of a native protein by a minimized binding domain.

Starovasnik, M.A.Braisted, A.C.Wells, J.A.

(1997) Proc Natl Acad Sci U S A 94: 10080-10085

  • DOI: https://doi.org/10.1073/pnas.94.19.10080
  • Primary Citation of Related Structures:  
    1ZDA, 1ZDB, 1ZDC, 1ZDD

  • PubMed Abstract: 

    The affinity between molecules depends both on the nature and presentation of the contacts. Here, we observe coupling of functional and structural elements when a protein binding domain is evolved to a smaller functional mimic. Previously, a 38-residue form of the 59-residue B-domain of protein A, termed Z38, was selected by phage display. Z38 contains 13 mutations and binds IgG only 10-fold weaker than the native B-domain. We present the solution structure of Z38 and show that it adopts a tertiary structure remarkably similar to that observed for the first two helices of B-domain in the B-domain/Fc complex [Deisenhofer, J. (1981) Biochemistry 20, 2361-2370], although it is significantly less stable. Based on this structure, we have improved on Z38 by designing a 34-residue disulfide-bonded variant (Z34C) that has dramatically enhanced stability and binds IgG with 9-fold higher affinity. The improved stability of Z34C led to NMR spectra with much greater chemical shift dispersion, resulting in a more precisely determined structure. Z34C, like Z38, has a structure virtually identical to the equivalent region from native protein A domains. The well-defined hydrophobic core of Z34C reveals key structural features that have evolved in this small, functional domain. Thus, the stabilized two-helix peptide, about half the size and having one-third of the remaining residues altered, accurately mimics both the structure and function of the native domain.


  • Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MINI PROTEIN A DOMAIN, Z3838synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 56 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST RESTRAINT VIOLATION ENERGY 

Structure Validation

View Full Validation Report

Currently 1ZDB does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations, Other