1SVX | pdb_00001svx

Crystal structure of a designed selected Ankyrin Repeat protein in complex with the Maltose Binding Protein

• PDB DOI: https://doi.org/10.2210/pdb1SVX/pdb

• Classification: de novo protein/sugar binding protein
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-30 Released: 2004-05-25 
• Deposition Author(s): Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Gruetter, M.G., Plueckthun, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.198 (DCC) 

Literature

High-affinity binders selected from designed ankyrin repeat protein libraries

Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Gruetter, M.G., Plueckthun, A.

(2004) Nat Biotechnol 22: 575-582

• PubMed: 15097997 
• DOI: https://doi.org/10.1038/nbt962
• Primary Citation Related Structures: 
  1SVX


• PubMed Abstract: 
  

  We report here the evolution of ankyrin repeat (AR) proteins in vitro for specific, high-affinity target binding. Using a consensus design strategy, we generated combinatorial libraries of AR proteins of varying repeat numbers with diversified binding surfaces. Libraries of two and three repeats, flanked by 'capping repeats,' were used in ribosome-display selections against maltose binding protein (MBP) and two eukaryotic kinases. We rapidly enriched target-specific binders with affinities in the low nanomolar range and determined the crystal structure of one of the selected AR proteins in complex with MBP at 2.3 A resolution. The interaction relies on the randomized positions of the designed AR protein and is comparable to natural, heterodimeric protein-protein interactions. Thus, our AR protein libraries are valuable sources for binding molecules and, because of the very favorable biophysical properties of the designed AR proteins, an attractive alternative to antibody libraries.

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Organizational Affiliation: 
• Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.5 kDa 
• Atom Count: 4,245 
• Modeled Residue Count: 526 
• Deposited Residue Count: 564 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin Repeat Protein off7	A	169	N/A	Mutation(s): 0  Gene Names: designed synthetic gene

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	B	395	Escherichia coli	Mutation(s): 0  Gene Names: MALE, B4034, Z5632, ECS5017
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.198 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.68	α = 90
b = 45.15	β = 107.24
c = 79.57	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Gruetter, M.G., Plueckthun, A.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references