8V9N image
Deposition Date 2023-12-08
Release Date 2024-10-02
Last Version Date 2024-11-06
Entry Detail
PDB ID:
8V9N
Keywords:
TRANSCRIPTION
Title:
Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
DNA molecule (Taxon ID: 2853804)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.78 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 1 21 1
8V9N validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*AP*TP*AP*GP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
Chain IDs:A (auth: C)
Chain Length:16
Number of Molecules:1
Biological Source:DNA molecule
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*TP*AP*T)-3')
Chain IDs:B (auth: D)
Chain Length:16
Number of Molecules:1
Biological Source:DNA molecule
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription factor PU.1
Gene (Uniprot):SPI1
Chain IDs:C (auth: F)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P17947 Pfam ID:PF00178
Primary Citation
Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics.
Rsc Adv 14 29675 29682 (2024)
PMID: 39297050 DOI: 10.1039/d4ra05957c

Abstact

The recognition of specific genomic arrangements by rationally designed small molecules is fundamental for the expansion of targeted gene expression. Here, we report the first X-ray crystal structures that demonstrate single G (guanine) recognition by a highly selective diamidine (DB2447) in a mixed DNA sequence. The study presents detailed structural information on the mechanism of single G recognition by D2447 and its various interactions in the DNA minor groove. Molecular dynamics and binding studies were used to evaluate the details of our reported structures. The study provides structural insight and resources necessary for understanding single G selection in genomic sequences.

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Primary Citation of related structures
8V9N