1ZDC

DISULFIDE-STABILIZED MINI PROTEIN A DOMAIN, Z34C, NMR, 24 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 48 
  • Conformers Submitted: 24 
  • Selection Criteria: LOWEST RESTRAINT VIOLATION ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 94: 10080-10085

  • DOI: 10.1073/pnas.94.19.10080
  • Primary Citation of Related Structures:  

  • 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-resid ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STABLE MINI PROTEIN A DOMAIN, Z34C
A
35N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A
NON-POLYMERH2 N

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 48 
  • Conformers Submitted: 24 
  • Selection Criteria: LOWEST RESTRAINT VIOLATION ENERGY 
  • Olderado: 1ZDC Olderado
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-07-09 
  • Released Date: 1997-09-17 
  • Deposition Author(s): Starovasnik, M.A.

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance