8V9N | pdb_00008v9n

Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history. 


Literature

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.

(2024) RSC Adv 14: 29675-29682

  • DOI: https://doi.org/10.1039/d4ra05957c
  • Primary Citation of Related Structures:  
    8V9N, 8VDH, 8VDI

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 
    • Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA wdw@gsu.edu +1 404-413-5505 +1 404-413-5503.

Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor PU.1C [auth F]106Homo sapiensMutation(s): 0 
Gene Names: SPI1
UniProt & NIH Common Fund Data Resources
Find proteins for P17947 (Homo sapiens)
Explore P17947 
Go to UniProtKB:  P17947
PHAROS:  P17947
GTEx:  ENSG00000066336 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17947
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*TP*AP*GP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')A [auth C]16DNA molecule
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*TP*AP*T)-3')B [auth D]16DNA molecule
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.928α = 90
b = 60.363β = 116.775
c = 44.707γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111749
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL155178
National Science Foundation (NSF, United States)United StatesMCB2028902
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137160

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references, Structure summary