3T6F

Biotin complex of Y54F core streptavidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Second-Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics.

Baugh, L.Le Trong, I.Cerutti, D.S.Mehta, N.Gulich, S.Stayton, P.S.Stenkamp, R.E.Lybrand, T.P.

(2012) Biochemistry 51: 597-607

  • DOI: https://doi.org/10.1021/bi201221j
  • Primary Citation of Related Structures:  
    3T6F, 3T6L

  • PubMed Abstract: 

    We report a point mutation in the second contact shell of the high-affinity streptavidin-biotin complex that appears to reduce binding affinity through transmitted effects on equilibrium dynamics. The Y54F streptavidin mutation causes a 75-fold loss of binding affinity with 73-fold faster dissociation, a large loss of binding enthalpy (ΔΔH = 3.4 kcal/mol at 37 °C), and a small gain in binding entropy (TΔΔS = 0.7 kcal/mol). The removed Y54 hydroxyl is replaced by a water molecule in the bound structure, but there are no observable changes in structure in the first contact shell and no additional changes surrounding the mutation. Molecular dynamics simulations reveal a large increase in the atomic fluctuation amplitudes for W79, a key biotin contact residue, compared to the fluctuation amplitudes in the wild-type. The increased W79 atomic fluctuation amplitudes are caused by loss of water-mediated hydrogen bonds between the Y54 hydroxyl group and peptide backbone atoms in and near W79. We propose that the increased atomic fluctuation amplitudes diminish the integrity of the W79-biotin interaction and represents a loosening of the "tryptophan collar" that is critical to the slow dissociation and high affinity of streptavidin-biotin binding. These results illustrate how changes in protein dynamics distal to the ligand binding pocket can have a profound impact on ligand binding, even when equilibrium structure is unperturbed.


  • Organizational Affiliation

    Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin
A, B
127Streptomyces avidiniiMutation(s): 1 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BSO
Query on BSO

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
BIOTIN-D-SULFOXIDE
C10 H16 N2 O4 S
KCSKCIQYNAOBNQ-OKPRWBIXSA-N
BTN
Query on BTN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
L [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BTN BindingDB:  3T6F Kd: 0 (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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.611α = 90
b = 94.114β = 90
c = 104.595γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description