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

  • Resolution: 1.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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This is version 1.3 of the entry. See complete history


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 157: 467-475

  • DOI: https://doi.org/10.1093/jb/mvv004
  • Primary Citation of Related Structures:  
    3WZN, 3WZO, 3WZP, 3WZQ

  • 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) 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
129Streptomyces avidiniiMutation(s): 8 
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
BTN BindingDB:  3WZN Kd: 1 (nM) from 1 assay(s)
ΔH: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.677α = 90
b = 54.344β = 90
c = 60.064γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description