1KTR

Crystal Structure of the Anti-His Tag Antibody 3D5 Single-Chain Fragment (scFv) in Complex with a Oligohistidine peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the anti-His tag antibody 3D5 single-chain fragment complexed to its antigen.

Kaufmann, M.Lindner, P.Honegger, A.Blank, K.Tschopp, M.Capitani, G.Pluckthun, A.Grutter, M.G.

(2002) J.Mol.Biol. 318: 135-147

  • DOI: 10.1016/S0022-2836(02)00038-4

  • PubMed Abstract: 
  • The crystal structure of a mutant form of the single-chain fragment (scFv), derived from the monoclonal anti-His tag antibody 3D5, in complex with a hexahistidine peptide has been determined at 2.7 A resolution. The peptide binds to a deep pocket for ...

    The crystal structure of a mutant form of the single-chain fragment (scFv), derived from the monoclonal anti-His tag antibody 3D5, in complex with a hexahistidine peptide has been determined at 2.7 A resolution. The peptide binds to a deep pocket formed at the interface of the variable domains of the light and the heavy chain, mainly through hydrophobic interaction to aromatic residues and hydrogen bonds to acidic residues. The antibody recognizes the C-terminal carboxylate group of the peptide as well as the main chain of the last four residues and the last three imidazole side-chains. The crystals have a solvent content of 77% (v/v) and form 70 A-wide channels that would allow the diffusion of peptides or even small proteins. The anti-His scFv crystals could thus act as a framework for the crystallization of His-tagged target proteins. Designed mutations in framework regions of the scFv lead to high-level expression of soluble protein in the periplasm of Escherichia coli. The recombinant anti-His scFv is a convenient detection tool when fused to alkaline phosphatase. When immobilized on a matrix, the antibody can be used for affinity purification of recombinant proteins carrying a very short tag of just three histidine residues, suitable for crystallization. The experimental structure is now the basis for the design of antibodies with even higher stability and affinity.


    Related Citations: 
    • Specific detection of his-tagged proteins with recombinant anti-His tag scFv-phosphatase or scFv-phage fusions
      Lindner, P.,Bauer, K.,Krebber, A.,Nieba, L.,Kremmer, E.,Krebber, C.,Honegger, A.,Klinger, B.,Mocikat, R.,Plueckthun, A.
      (1997) BIO*TECHNIQUES 22: 140


    Organizational Affiliation

    Biochemisches Institut, Universit├Ąt Z├╝rich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-his tag antibody 3d5 variable light chain
L
116N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide linker
M
20N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Anti-his tag antibody 3d5 variable heavy chain
H
114Mus musculusGene Names: VH186.2-D-J-C mu
Find proteins for Q924R5 (Mus musculus)
Go to UniProtKB:  Q924R5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Oligohistidine peptide Antigen
P
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.510α = 90.00
b = 106.510β = 90.00
c = 92.800γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance