8QHM | pdb_00008qhm

DNA mimic Foldamer with sticky ends

• PDB DOI: https://doi.org/10.2210/pdb8QHM/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2023-09-08 Released: 2023-10-11 
• Deposition Author(s): Deepak, D., Loos, M., Huc, I.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.381 (Depositor), 0.375 (DCC) 
• R-Value Work: 
  0.347 (Depositor), 0.349 (DCC) 
• R-Value Observed: 
  0.349 (Depositor) 

Starting Model: other

Literature

Enhancing the Features of DNA Mimic Foldamers for Structural Investigations.

Corvaglia, V., Wu, J., Deepak, D., Loos, M., Huc, I.

(2024) Chemistry 30: e202303650-e202303650

• PubMed: 38193643 
• DOI: https://doi.org/10.1002/chem.202303650
• Primary Citation Related Structures: 
  8QHM


• PubMed Abstract: 
  

  DNA mimic foldamers based on aromatic oligoamide helices bearing anionic phosphonate side chains have been shown to bind to DNA-binding proteins sometimes orders of magnitude better than DNA itself. Here, we introduce new features in the DNA mimic foldamers to facilitate structural investigations of their interactions with proteins. Thirteen new foldamer sequences have been synthesized and characterized using NMR, circular dichroism, molecular modeling, and X-ray crystallography. The results show that foldamer helix handedness can be quantitatively biased by means of a single stereogenic center, that the foldamer structure can be made C ₂ -symmetrical as in palindromic B-DNA sequences, and that associations between foldamer helices can be promoted utilizing dedicated C-terminal residues that act as sticky ends in B-DNA structures.

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Organizational Affiliation: 
• Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.
Current address: Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Italy) & Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, 20162, Milan, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.23 kDa 
• Atom Count: 609 
• Modeled Residue Count: 33 
• Deposited Residue Count: 34 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mimic Foldamer	A, B [auth F]	17	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
9JV	A, B [auth F]	L-PEPTIDE LINKING	C11 H10 N2 O3		--
QVE	A, B [auth F]	L-PEPTIDE LINKING	C12 H10 N2 O5		--
V4F	A, B [auth F]	PEPTIDE LINKING	C12 H13 N2 O6 P		V4F
V53	A, B [auth F]	PEPTIDE LINKING	C11 H11 N2 O6 P		ES1
V5F	A, B [auth F]	PEPTIDE LINKING	C9 H11 N O3		--
VNW	A, B [auth F]	PEPTIDE LINKING	C11 H10 N2 O2 Se		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.381 (Depositor), 0.375 (DCC) 
• R-Value Work:  0.347 (Depositor), 0.349 (DCC) 
• R-Value Observed: 0.349 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.146	α = 90
b = 74.146	β = 90
c = 83.693	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Deepak, D., Loos, M., Huc, I.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-04-24
  Changes: Database references
• Version 2.2: 2024-09-04
  Changes: Data collection