1H0T | pdb_00001h0t

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

• PDB DOI: https://doi.org/10.2210/pdb1H0T/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Staphylococcus aureus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-06-27 Released: 2003-02-27 
• Deposition Author(s): Wahlberg, E., Lendel, C., Helgstrand, M., Allard, P., Dincbas-Renqvist, V., Hedqvist, A., Berglund, H., Nygren, P.-A., Hard, T.

---

Experimental Data Snapshot

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

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

• PubMed: 12594333 
• DOI: https://doi.org/10.1073/pnas.0436086100
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.1 kDa 
• Atom Count: 924 
• Modeled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN G BINDING PROTEIN A	A	58	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ZSPA-1 AFFIBODY	B	58	synthetic construct	Mutation(s): 0

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

Entry History 

Deposition Data

• Released Date: 2003-02-27 
Deposition Author(s): Wahlberg, E., Lendel, C., Helgstrand, M., Allard, P., Dincbas-Renqvist, V., Hedqvist, A., Berglund, H., Nygren, P.-A., Hard, T.

Revision History  

• 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