4HQU

Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer SL5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.

Davies, D.R.Gelinas, A.D.Zhang, C.Rohloff, J.C.Carter, J.D.O'Connell, D.Waugh, S.M.Wolk, S.K.Mayfield, W.S.Burgin, A.B.Edwards, T.E.Stewart, L.J.Gold, L.Janjic, N.Jarvis, T.C.

(2012) Proc Natl Acad Sci U S A 109: 19971-19976

  • DOI: 10.1073/pnas.1213933109
  • Primary Citation of Related Structures:  
    4HQU, 4HQX

  • PubMed Abstract: 
  • Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids ...

    Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.


    Organizational Affiliation

    Emerald BioStructures, Inc, Bainbridge Island, WA 98110, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet-derived growth factor subunit B A109Homo sapiensMutation(s): 0 
Gene Names: PDGFBPDGF2SIS
Find proteins for P01127 (Homo sapiens)
Explore P01127 
Go to UniProtKB:  P01127
NIH Common Fund Data Resources
PHAROS:  P01127
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
SOMAmer SL5C24N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.71α = 90
b = 59.71β = 90
c = 167.01γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references