8EO4

Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) with Di-methylated CpG sites

  • Classification: TRANSCRIPTION/DNA
  • Organism(s): synthetic construct, Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-10-02 Released: 2023-07-05 
  • Deposition Author(s): Terrell, J.R., Poon, G.M.K.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DNA selection by the master transcription factor PU.1.

Terrell, J.R.Taylor, S.J.Schneider, A.L.Lu, Y.Vernon, T.N.Xhani, S.Gumpper, R.H.Luo, M.Wilson, W.D.Steidl, U.Poon, G.M.K.

(2023) Cell Rep 42: 112671-112671

  • DOI: https://doi.org/10.1016/j.celrep.2023.112671
  • Primary Citation of Related Structures:  
    8E3K, 8E3R, 8E4H, 8E5Y, 8EBH, 8EE9, 8EJ6, 8EJ8, 8EK3, 8EK8, 8EKJ, 8EKU, 8EKV, 8EKZ, 8EM9, 8EMD, 8ENG, 8EO1, 8EO4, 8EQG, 8EQK, 8EQL

  • PubMed Abstract: 

    The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.


  • Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.


Macromolecules

Find similar proteins by:  (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*AP*GP*CP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')A [auth C]16synthetic construct
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*GP*CP*TP*TP*AP*T)-3')B [auth D]16synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.905α = 90
b = 60.675β = 116.814
c = 44.538γ = 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 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111749

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description