Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46860.50 
• Atom Count: 2862 
• Residue Count: 296 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4ZBN

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

• DOI: 10.2210/pdb4ZBN/pdb
• NDB: 4ZBN

• Classification: Immune system/DNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2015-04-15 Released: 2015-06-10 
• Deposition Author(s): Davies, D.R., Edwards, T.E.

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Experimental Data Snapshot

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

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

• PubMed: 26027732 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-nerve growth factor	A, B	120	Homo sapiens	Mutation(s): 0  Gene Names: NGF (NGFB)
Find proteins for P01138 (Homo sapiens) Go to Gene View: NGF Go to UniProtKB:  P01138

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (28-MER)	D,E	28	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	D	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DUZ	D, E	DNA linking	C17 H20 N3 O9 P		DU

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 = 109.201	α = 90.00
b = 60.708	β = 95.57
c = 68.589	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-15 
• Released Date: 2015-06-10 
• Deposition Author(s): Davies, D.R., Edwards, T.E.

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