8QPC | pdb_00008qpc

18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein

• PDB DOI: https://doi.org/10.2210/pdb8QPC/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Sulfolobus acidocaldarius, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-01 Released: 2023-11-08 
• Deposition Author(s): Deepak, D., Corvaglia, V., Wu, J., Huc, I.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 
  0.348 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.336 (Depositor), 0.350 (DCC) 
• R-Value Observed: 
  0.336 (Depositor) 

Starting Model: experimental

Literature

DNA Mimic Foldamer Recognition of a Chromosomal Protein.

Deepak, D., Wu, J., Corvaglia, V., Allmendinger, L., Scheckenbach, M., Tinnefeld, P., Huc, I.

(2025) Angew Chem Int Ed Engl 64: e202422958-e202422958

• PubMed: 39714421 
• DOI: https://doi.org/10.1002/anie.202422958
• Primary Citation of Related Structures:  
  8CMN, 8Q2M, 8QPC


• PubMed Abstract: 
  

  Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked.

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Organizational Affiliation: 
• Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, 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, Milan, Italy.
Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 12.66 kDa 
• Atom Count: 812 
• Modeled Residue Count: 83 
• Deposited Residue Count: 86 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein 7b	A [auth AA]	66	Sulfolobus acidocaldarius	Mutation(s): 2  Gene Names: Saci_0064
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore P13123  Go to UniProtKB:  P13123

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide	B	10	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide	C	10	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DBU	B	PEPTIDE LINKING	C4 H7 N O2		THR
V4F	B	PEPTIDE LINKING	C12 H13 N2 O6 P		V4F
V53	B	PEPTIDE LINKING	C11 H11 N2 O6 P		ES1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free:  0.348 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.336 (Depositor), 0.350 (DCC) 
• R-Value Observed: 0.336 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.907	α = 90
b = 70.907	β = 90
c = 121.997	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Deepak, D., Corvaglia, V., Wu, J., Huc, I.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	325871075 (CRC1309-C7)
European Research Council (ERC)	European Union	ERC-2021-ADG-320892

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 3.0: 2024-05-01
  Changes: Atomic model, Polymer sequence
• Version 3.1: 2025-01-22
  Changes: Database references, Structure summary
• Version 3.2: 2025-02-26
  Changes: Database references