3VHI

Crystal structure of monoZ-biotin-avidin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational development of caged-biotin protein-labeling agents and some applications in live cells

Terai, T.Maki, E.Sugiyama, S.Takahashi, Y.Matsumura, H.Mori, Y.Nagano, T.

(2011) Chem.Biol. 18: 1261-1272

  • DOI: 10.1016/j.chembiol.2011.09.007
  • Primary Citation of Related Structures:  3VGW, 3VHH, 3VHM

  • PubMed Abstract: 
  • Biotin-(strept)avidin complex is widely used in biotechnology because of its extremely high binding constant, but there is no report describing spatiotemporally controlled formation of the complex in live cells. Here, based on X-ray crystal structure ...

    Biotin-(strept)avidin complex is widely used in biotechnology because of its extremely high binding constant, but there is no report describing spatiotemporally controlled formation of the complex in live cells. Here, based on X-ray crystal structure analysis and calorimetric data, we designed and synthesized photoreleasable biotins, which show greatly reduced affinity for (strept)avidin, but recover native affinity after UV irradiation. For application at the cell surface, we introduced an amine-reactive moiety into these "caged" biotin molecules. Specific fluorescence imaging of live cells that had been labeled with these agents and then UV-irradiated, was accomplished by addition of streptavidin conjugated with a fluorophore. We also demonstrated the applicability of these compounds for UV-irradiated-cell-specific drug delivery by using caged-biotin-labeled cells, a prodrug, and streptavidin conjugated with a prodrug-activating enzyme.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Avidin
A, B, C, D
122Gallus gallusGene Names: AVD
Find proteins for P02701 (Gallus gallus)
Go to UniProtKB:  P02701
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B, C, D
5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid
C18 H22 N2 O5 S
BWNGWJMPVBQLHD-DZKIICNBSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VHIKa: 2300000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.781α = 90.00
b = 73.455β = 120.05
c = 81.251γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description