ISDA

Deposition Date 2023-12-15

Release Date 2024-09-18

Last Version Date 2024-11-13

Entry Detail

PDB ID:

8VDH

Keywords:

TRANSCRIPTION/DNA

Title:

Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG) in Ternary Complex with DB2447

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:

1.64 Å

R-Value Free:

0.20

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 1 21 1

Download 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

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

Ligand Molecules

A1AAQ

Primary Citation

Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics.

Ogbonna, E.N, Terrell, J.R, Paul, A, Farahat, A.A, Poon, G.M.K, Boykin, D.W, Wilson, W.D.Show

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