4HQU

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 

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.USA 109: 19971-19976

  • DOI: 10.1073/pnas.1213933109
  • Primary Citation of Related Structures:  

  • 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 d ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet-derived growth factor subunit B
A
109Homo sapiensMutation(s): 0 
Gene Names: PDGFB (PDGF2, SIS)
Find proteins for P01127 (Homo sapiens)
Go to Gene View: PDGFB
Go to UniProtKB:  P01127
Entity ID: 2
MoleculeChainsLengthOrganism
SOMAmer SL5C24N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
C
RNA LINKINGC11 H16 N5 O7 PA
PE6
Query on PE6
C
NON-POLYMERC12 H27 O10 P

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18M
Query on 18M
C
RNA linkingC11 H17 N5 O11 P2G
UPE
Query on UPE
C
DNA linkingC18 H22 N3 O9 PDU
DUZ
Query on DUZ
C
DNA linkingC17 H20 N3 O9 PDU
18Q
Query on 18Q
C
DNA linkingC15 H18 N3 O9 P SDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.710α = 90.00
b = 59.710β = 90.00
c = 167.010γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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