3WZN

Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin at 1.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of a streptavidin mutant specific for an artificial biotin analogue

Kawato, T.Mizohata, E.Shimizu, Y.Meshizuka, T.Yamamoto, T.Takasu, N.Matsuoka, M.Matsumura, H.Kodama, T.Kanai, M.Doi, H.Inoue, T.Sugiyama, A.

(2015) J.Biochem. --: --

  • DOI: 10.1093/jb/mvv004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For a multistep pre-targeting method using antibodies, a streptavidin mutant with low immunogenicity, termed low immunogenic streptavidin mutant No. 314 (LISA-314), was produced previously as a drug delivery tool. However, endogenous biotins (BTNs) w ...

    For a multistep pre-targeting method using antibodies, a streptavidin mutant with low immunogenicity, termed low immunogenic streptavidin mutant No. 314 (LISA-314), was produced previously as a drug delivery tool. However, endogenous biotins (BTNs) with high affinity (Kd < 10(-10) M) for the binding pocket of LISA-314 prevents access of exogenous BTN-labelled anticancer drugs. In this study, we improve the binding pocket of LISA-314 to abolish its affinity for endogenous BTN species, therefore ensuring that the newly designed LISA-314 binds only artificial BTN analogue. The replacement of three amino acid residues was performed in two steps to develop a mutant termed V212, which selectively binds to 6-(5-((3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamido)hexanoic acid (iminobiotin long tail, IMNtail). Surface plasmon resonance results showed that V212 has a Kd value of 5.9 × 10(-7) M towards IMNtail, but no binding affinity for endogenous BTN species. This V212/IMNtail system will be useful as a novel delivery tool for anticancer therapy.


    Organizational Affiliation

    Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B
129Streptomyces avidiniiMutation(s): 8 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BTN
Query on BTN

Download SDF File 
Download CCD File 
A, B
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNKd: 1 nM (93) BINDINGDB
BTNΔH: -66.9 - -123 kJ/mol (93) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.677α = 90.00
b = 54.344β = 90.00
c = 60.064γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SERGUIdata collection
PHASERphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description