4ZBN

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.447 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor.

Jarvis, T.C.Davies, D.R.Hisaminato, A.Resnicow, D.I.Gupta, S.Waugh, S.M.Nagabukuro, A.Wadatsu, T.Hishigaki, H.Gawande, B.Zhang, C.Wolk, S.K.Mayfield, W.S.Nakaishi, Y.Burgin, A.B.Stewart, L.J.Edwards, T.E.Gelinas, A.D.Schneider, D.J.Janjic, N.

(2015) Structure 23: 1293-1304

  • DOI: 10.1016/j.str.2015.03.027

  • PubMed Abstract: 
  • Discerning the structural building blocks of macromolecules is essential for understanding their folding and function. For a new generation of modified nucleic acid ligands (called slow off-rate modified aptamers or SOMAmers), we previously observed ...

    Discerning the structural building blocks of macromolecules is essential for understanding their folding and function. For a new generation of modified nucleic acid ligands (called slow off-rate modified aptamers or SOMAmers), we previously observed essential functions of hydrophobic aromatic side chains in the context of well-known nucleic acid motifs. Here we report a 2.45-Å resolution crystal structure of a SOMAmer complexed with nerve growth factor that lacks any known nucleic acid motifs, instead adopting a configuration akin to a triangular prism. The SOMAmer utilizes extensive hydrophobic stacking interactions, non-canonical base pairing and irregular purine glycosidic bond angles to adopt a completely non-helical, compact S-shaped structure. Aromatic side chains contribute to folding by creating an unprecedented intercalating zipper-like motif and a prominent hydrophobic core. The structure provides compelling rationale for potent inhibitory activity of the SOMAmer and adds entirely novel motifs to the repertoire of structural elements uniquely available to SOMAmers.


    Organizational Affiliation

    SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-nerve growth factor
A, B
120Homo sapiensMutation(s): 0 
Gene Names: NGF (NGFB)
Find proteins for P01138 (Homo sapiens)
Go to Gene View: NGF
Go to UniProtKB:  P01138
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (28-MER)D,E28synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DUZ
Query on DUZ
D, E
DNA linkingC17 H20 N3 O9 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.447 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.201α = 90.00
b = 60.708β = 95.57
c = 68.589γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references
  • Version 1.2: 2015-07-15
    Type: Database references