3VDZ

Tailoring Encodable Lanthanide-Binding Tags as MRI Contrast Agents: xq-dSE3-Ubiquitin at 2.4 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Tailoring encodable lanthanide-binding tags as MRI contrast agents.

Daughtry, K.D.Martin, L.J.Sarraju, A.Imperiali, B.Allen, K.N.

(2012) Chembiochem 13: 2567-2574

  • DOI: 10.1002/cbic.201200448
  • Primary Citation of Related Structures:  
    3VDZ

  • PubMed Abstract: 
  • Lanthanide-binding tags (LBTs), peptide-based coexpression tags with high affinity for lanthanide ions, have previously been applied as luminescent probes to provide phasing for structure determination in X-ray crystallography and to provide restraints for structural refinement and distance information in NMR ...

    Lanthanide-binding tags (LBTs), peptide-based coexpression tags with high affinity for lanthanide ions, have previously been applied as luminescent probes to provide phasing for structure determination in X-ray crystallography and to provide restraints for structural refinement and distance information in NMR. The native affinity of LBTs for Gd(3+) indicates their potential as the basis for engineering of peptide-based MRI agents. However, the lanthanide coordination state that enhances luminescence and affords tightest binding would not be ideal for applications of LBTs as contrast agents, due to the exclusion of water from the inner coordination sphere. Herein, we use structurally defined LBTs as the starting point for re-engineering the first coordination shell of the lanthanide ion to provide for high contrast through direct coordination of water to Gd(3+) (resulting in the single LBT peptide, m-sLBT). The effectiveness of LBTs as MRI contrast agents was examined in vitro through measurement of binding affinity and proton relaxivity. For imaging applications that require targeted observation, fusion to specific protein partners is desirable. However, a fusion protein comprising a concatenated double LBT (dLBT) as an N-terminal tag for the model protein ubiquitin had reduced relaxivity compared with the free dLBT peptide. This limitation was overcome by the use of a construct based on the m-sLBT sequence (q-dLBT-ubiquitin). The structural basis for the enhanced contrast was examined by comparison of the X-ray crystal structure of xq-dLBT-ubiquitin (wherein two tryptophan residues are replaced with serine), to that of dLBT-ubiquitin. The structure shows that the backbone conformational dynamics of the MRI variant may allow enhanced water exchange. This engineered LBT represents a first step in expanding the current base of specificity-targeted agents available.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02218, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aA, B111synthetic constructHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.166α = 90
b = 46.166β = 90
c = 113.552γ = 120
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
SOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Data collection, Derived calculations