8D86 | pdb_00008d86

Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence co-crystallized with a guest small molecule, netropsin.

PDB DOI: https://doi.org/10.2210/pdb8D86/pdb
NAKB: 8D86

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Escherichia coli, Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-06-07 Released: 2023-06-28
Deposition Author(s): Orun, A.R., Snow, C.D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds.

Orun, A.R., Shields, E.T., Dmytriw, S., Vajapayajula, A., Slaughter, C.K., Snow, C.D.

(2023) ACS Nano 17: 13110-13120

PubMed: 37407546 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsnano.2c07282
Primary Citation Related Structures:
7SDP, 7SOZ, 7U6K, 7U7O, 7UFX, 7UOG, 7UR0, 7UV6, 7UV7, 7UXY, 8D86

PubMed Abstract:
High-precision nanomaterials to entrap DNA-binding molecules are sought after for applications such as controlled drug delivery and scaffold-assisted structural biology. Here, we engineered protein-DNA cocrystals to serve as scaffolds for DNA-binding molecules. The designed cocrystals, isoreticular cocrystals, contain DNA-binding protein and cognate DNA blocks where the DNA-DNA junctions stack end-to-end. Furthermore, the crystal symmetry allows topology preserving (isoreticular) expansion of the DNA stack without breaking protein-protein contacts, hence providing larger solvent channels for guest diffusion. Experimentally, the resulting designed isoreticular cocrystal adopted an interpenetrating I 222 lattice, a phenomenon previously observed in metal-organic frameworks (MOFs). The interpenetrating lattice crystallized dependably in the same space group despite myriad modifications at the DNA-DNA junctions. Assembly was modular with respect to the DNA inserted for expansion, providing an interchangeable DNA sequence for guest-specified scaffolding. Also, the DNA-DNA junctions were tunable, accommodating varied sticky base overhang lengths and terminal phosphorylation. As a proof of concept, we used the interpenetrating scaffold crystals to separately entrap three distinct guest molecules during crystallization. Isoreticular cocrystal design offers a route to a programmable scaffold for DNA-binding molecules, and the design principles may be applied to existing cocrystals to develop scaffolding materials.

Organizational Affiliation

Department of Chemistry, Colorado State University, 1301 Center Ave., Fort Collins, Colorado 80523, United States.

Macromolecule Content

Total Structure Weight: 51 kDa
Atom Count: 3,141
Modeled Residue Count: 278
Deposited Residue Count: 327
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication initiation protein	C	263	Escherichia coli K-12	Mutation(s): 1 Gene Names: repE, E, rep, ECOK12F045
UniProt
Find proteins for P03856 (Escherichia coli (strain K12)) Explore P03856 Go to UniProtKB: P03856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03856
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(ACPCPCPGPGPAPCPCPTPGPTPGPAPCPAPAPAPTPTPGPCPCPCPTPCPAPGPAPCPGP*G)-3')	A	32	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(AGPGPCPCPGPTPCPTPGPAPGPGPGPCPAPAPTPTPTPGPTPCPAPCPAPGPGPTPCPCP*G)-3')	B	32	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NT (Subject of Investigation/LOI) Query on NT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	NETROPSIN C₁₈ H₂₆ N₁₀ O₃ IDBIFFKSXLYUOT-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C]