3WYP

Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of streptavidin mutant with low immunogenicity

Kawato, T.Mizohata, E.Meshizuka, T.Doi, H.Kawamura, T.Matsumura, H.Yumura, K.Tsumoto, K.Kodama, T.Inoue, T.Sugiyama, A.

(2014) J.Biosci.Bioeng. --: --

  • DOI: 10.1016/j.jbiosc.2014.10.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We previously created a low-immunogenic core streptavidin mutant No. 314 (LISA-314) by replacing six amino-acid residues for use as a delivery tool for an antibody multistep pre-targeting process (Yumura et al., Protein Sci., 22, 213-221, 2013). Here ...

    We previously created a low-immunogenic core streptavidin mutant No. 314 (LISA-314) by replacing six amino-acid residues for use as a delivery tool for an antibody multistep pre-targeting process (Yumura et al., Protein Sci., 22, 213-221, 2013). Here, we performed high-resolution X-ray structural analyses of LISA-314 and wild-type streptavidin to investigate the effect of substitutions on the protein function and the three-dimensional structure. LISA-314 forms a tetramer in the same manner as wild-type streptavidin. The binding mode of d-biotin in LISA-314 is also completely identical to that in wild-type streptavidin, and conformational changes were observed mostly at the side chains of substituted sites. Any large conformational changes corresponding to the reduction of B factors around the substituted sites were not observed. These results demonstrated the LISA-314 acquired low immunogenicity without losing structural properties of original wild-type streptavidin.


    Organizational Affiliation

    Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: sugiyama@lsbm.org.,Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B, D, C
127Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BSO
Query on BSO

Download SDF File 
Download CCD File 
B, C
BIOTIN-D-SULFOXIDE
5-[(3AR,4R,6AS)-5-OXIDO-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID
C10 H16 N2 O4 S
KCSKCIQYNAOBNQ-OKPRWBIXSA-N
 Ligand Interaction
BTN
Query on BTN

Download SDF File 
Download CCD File 
A, D
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNΔH: -66.9 - -123 kJ/mol (100) BINDINGDB
BTNKd: 1 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.354α = 90.00
b = 97.696β = 112.29
c = 52.570γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
BSSdata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release