4BJ8

Zebavidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Zebavidin

Niederhauser, B.Zmurko, J.Parthiban, M.Ojanen, M.Kukkurainen, S.Maatta, J.A.E.Leppiniemi, J.Janis, J.Parikka, M.Turpeinen, H.Pesu, M.Johnson, M.S.Airenne, T.T.Kulomaa, M.S.Hytonen, V.P.

(2013) PLoS One 8: 77207

  • DOI: https://doi.org/10.1371/journal.pone.0077207
  • Primary Citation of Related Structures:  
    4BJ8

  • PubMed Abstract: 

    The avidin protein family members are well known for their high affinity towards D-biotin and high structural stability. These properties make avidins valuable tools for a wide range of biotechnology applications. We have identified a new member of the avidin family in the zebrafish (Danio rerio) genome, hereafter called zebavidin. The protein is highly expressed in the gonads of both male and female zebrafish and in the gills of male fish, but our data suggest that zebavidin is not crucial for the developing embryo. Biophysical and structural characterisation of zebavidin revealed distinct properties not found in any previously characterised avidins. Gel filtration chromatography and native mass spectrometry suggest that the protein forms dimers in the absence of biotin at low ionic strength, but assembles into tetramers upon binding biotin. Ligand binding was analysed using radioactive and fluorescently labelled biotin and isothermal titration calorimetry. Moreover, the crystal structure of zebavidin in complex with biotin was solved at 2.4 Å resolution and unveiled unique ligand binding and subunit interface architectures; the atomic-level details support our physicochemical observations.


  • Organizational Affiliation

    Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland ; Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ZEBAVIDIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
126Danio rerioMutation(s): 0 
UniProt
Find proteins for E7F650 (Danio rerio)
Explore E7F650 
Go to UniProtKB:  E7F650
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7F650
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download Ideal Coordinates CCD File 
AA [auth K]
BA [auth L]
DA [auth M]
EA [auth N]
FA [auth O]
AA [auth K],
BA [auth L],
DA [auth M],
EA [auth N],
FA [auth O],
GA [auth P],
Q [auth A],
R [auth B],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth H],
Y [auth I],
Z [auth J]
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth L]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BTN PDBBind:  4BJ8 Kd: 5.13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.24α = 90
b = 196.84β = 90
c = 52.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary