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 9PFO | pdb_00009pfo

Structure of POU2F3 POU domains bound to coactivator OCA-T2 and DNA (2.1 angstrom resolution)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.259 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PFO

This is version 1.2 of the entry. See complete history. 

Literature

Structural basis of DNA-dependent coactivator recruitment by the tuft cell master regulator POU2F3.

Alpsoy, A., Ipsaro, J.J., Skopelitis, D., Pal, S., Chung, F.S., Carpenter, S., Desmarais, J.J., Wu, X.S., Chang, K., DiMare, M.T., Harten, E., Bergman, S., Kinney, J.B., Engelman, J.A., Bhang, H.C., Joshua-Tor, L., Vakoc, C.R.

(2025) Cell Rep 44: 116572-116572

  • DOI: https://doi.org/10.1016/j.celrep.2025.116572
  • Primary Citation Related Structures: 
    9PFN, 9PFO, 9PFP

  • PubMed Abstract: 

    The transcription factor POU2F3 defines the identity of tuft cells and underlies a distinct molecular subtype of small cell lung cancer (SCLC). Although POU2F3 is considered undruggable, its activity critically depends on the coactivators OCA-T1 and OCA-T2. Here, we demonstrate that acute suppression of either POU2F3 or OCA-T1 induces regression of tuft cell-like SCLC xenografts in vivo. To explore the structural basis and druggability of this dependency, we determine crystal structures of POU2F3 bound to OCA-T1 or OCA-T2 in complex with DNA, revealing a tripartite, DNA-dependent interface. We further employ deep mutational scanning to assess the functional impact of 4,218 missense variants in POU2F3 and OCA-T1, uncovering both mutation-sensitive hotspots and structurally constrained regions critical for tumor cell fitness. These findings define a transcriptional complex that integrates DNA recognition with coactivator recruitment and nominate POU2F3-OCA-T as a structurally tractable vulnerability in tuft cell-like carcinomas.


  • Organizational Affiliation: 
    • Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Macromolecule Content 

  • Total Structure Weight: 127.59 kDa 
  • Atom Count: 8,679 
  • Modeled Residue Count: 785 
  • Deposited Residue Count: 916 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
POU domain, class 2, transcription factor 3
A, E, I, M
160Homo sapiensMutation(s): 0 
Gene Names: POU2F3, OTF11, PLA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKI9 (Homo sapiens)
Explore Q9UKI9 
Go to UniProtKB:  Q9UKI9
PHAROS:  Q9UKI9
GTEx:  ENSG00000137709 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKI9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
POU class 2 homeobox associating factor 3
B, F, J, N
39Homo sapiensMutation(s): 0 
Gene Names: POU2AF3, C11orf93, CASC13, COLCA2
UniProt & NIH Common Fund Data Resources
Find proteins for A8K830 (Homo sapiens)
Explore A8K830 
Go to UniProtKB:  A8K830
PHAROS:  A8K830
GTEx:  ENSG00000214290 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8K830
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA containing POU domain recognition element octamer (sense strand)
C, G, K, O
15Homo sapiens
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA containing POU domain recognition element octamer (antisense strand)
D, H, L, P
15Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.019α = 90
b = 95.802β = 101.24
c = 85.637γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
MolProbitymodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA045508
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA013106
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA242919
Department of Defense (DOD, United States)United StatesW81XWH1910317
Howard Hughes Medical Institute (HHMI)United States--
Other privateCold Spring Harbor Laboratory and Northwell Health Affiliation
Other privatePershing Square Sohn Cancer Research Alliance
Other privateTreeline Biosciences

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references
  • Version 1.2: 2025-12-10
    Changes: Database references