Biological Assembly 1  

 3D View: Structure | Electron Density

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.19 kDa 
• Atom Count: 1875 
• Residue Count: 234 
• Unique protein chains: 3

1P4B

Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P).

• DOI: 10.2210/pdb1P4B/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-04-22 Released: 2004-05-04 
• Deposition Author(s): Zahnd, C., Spinelli, S., Luginbuhl, B., Jermutus, L., Amstutz, P., Cambillau, C., Pluckthun, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.300 
• R-Value Work: 0.219 
• R-Value Observed: 0.230 

Literature

Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity.

Zahnd, C., Spinelli, S., Amstutz, P., Cambillau, C.

(2004) J Biol Chem 279: 18870-18877

• PubMed: 14754898 
• DOI: 10.1074/jbc.M309169200
• Primary Citation of Related Structures:  
  1P4I, 1P4B


• PubMed Abstract: 
  

We generated a single chain Fv fragment of an antibody (scFv) with a binding affinity of about 5 pm to a short peptide by applying rigorous directed evolution. Starting from a high affinity peptide binder, originally obtained by ribosome display from a murine library, we generated libraries of mutants with error-prone PCR and DNA shuffling and applied off-rate selection by using ribosome display. Crystallographic analysis of the scFv in its antigen-bound and free state showed that only few mutations, which do not make direct contact to the antigen, lead to a 500-fold affinity improvement over its potential germ line precursor. These results suggest that the affinity optimization of very high affinity binders is achieved by modulating existing interactions via subtle changes in the framework rather than by introducing new contacts. Off-rate selection in combination with ribosome display can evolve binders to the low picomolar affinity range even for peptide targets.

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Organizational Affiliation: 

Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Variable light chain	L	135	Mus musculus	Mutation(s): 0
Find proteins for P01723 (Mus musculus) Explore P01723  Go to UniProtKB:  P01723

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Variable heavy chain	H	124	Mus musculus	Mutation(s): 0
Find proteins for P01820 (Mus musculus) Explore P01820  Go to UniProtKB:  P01820

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4(7P-14P) peptide	P	12	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.300 
• R-Value Work: 0.219 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.238	α = 90
b = 36.291	β = 90.5
c = 84.455	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

• Deposited Date: 2003-04-22 
• Released Date: 2004-05-04 
Deposition Author(s): Zahnd, C., Spinelli, S., Luginbuhl, B., Jermutus, L., Amstutz, P., Cambillau, C., Pluckthun, A.

Revision History 

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance