7sdp image
Deposition Date 2021-09-29
Release Date 2021-10-13
Last Version Date 2023-11-01
Entry Detail
PDB ID:
7SDP
Title:
Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates.
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.01 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)-3')
Chain IDs:A
Chain Length:22
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)-3')
Chain IDs:B
Chain Length:22
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:RepB family plasmid replication initiator protein
Mutations:R118P
Chain IDs:C
Chain Length:263
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Unknown polymer fragment
Chain IDs:E (auth: D)
Chain Length:4
Number of Molecules:1
Biological Source:Eschericia coli
Polymer Type:polypeptide(L)
Molecule:Unknown polymer fragment
Chain IDs:D (auth: F)
Chain Length:3
Number of Molecules:1
Biological Source:Eschericia coli
Ligand Molecules
Primary Citation

Abstact

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 I222 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.

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Primary Citation of related structures