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- PDB-9pfn: Structure of POU2F3 POU domains bound to coactivator OCA-T2 and D... -

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Basic information

Entry
Database: PDB / ID: 9pfn
TitleStructure of POU2F3 POU domains bound to coactivator OCA-T2 and DNA (2.8 angstrom resolution)
Components
  • DNA containing POU domain recognition element octamer (antisense strand)
  • DNA containing POU domain recognition element octamer (sense strand)
  • POU class 2 homeobox associating factor 3
  • POU domain, class 2, transcription factor 3
KeywordsTRANSCRIPTION / transcription factor / DNA binding / coactivator complex
Function / homology
Function and homology information


POU domain binding / host-mediated suppression of viral transcription / epidermis development / keratinocyte differentiation / wound healing / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...POU domain binding / host-mediated suppression of viral transcription / epidermis development / keratinocyte differentiation / wound healing / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Colorectal cancer-associated protein 2 / : / OCA domain profile. / Octamer-binding transcription factor / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. ...Colorectal cancer-associated protein 2 / : / OCA domain profile. / Octamer-binding transcription factor / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / POU class 2 homeobox associating factor 3 / POU domain, class 2, transcription factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsIpsaro, J.J. / Alpsoy, A. / Vakoc, C.R. / Joshua-Tor, L.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA045508 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA013106 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA242919 United States
Department of Defense (DOD, United States)W81XWH1910317 United States
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
CitationJournal: To Be Published
Title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3
Authors: Alpsoy, A. / Ipsaro, J.J. / Skopelitis, D. / Pal, S. / Chung, F.S. / Carpenter, S. / Desmarais, J. / Wu, X.S. / Chang, K. / DiMare, M.T. / Harten, E. / Bergman, S. / Kinney, J. / Engelman, J. ...Authors: Alpsoy, A. / Ipsaro, J.J. / Skopelitis, D. / Pal, S. / Chung, F.S. / Carpenter, S. / Desmarais, J. / Wu, X.S. / Chang, K. / DiMare, M.T. / Harten, E. / Bergman, S. / Kinney, J. / Engelman, J.A. / Bhang, H.C. / Joshua-Tor, L. / Vakoc, C.R.
History
DepositionJul 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POU domain, class 2, transcription factor 3
B: POU class 2 homeobox associating factor 3
C: DNA containing POU domain recognition element octamer (sense strand)
D: DNA containing POU domain recognition element octamer (antisense strand)
E: POU domain, class 2, transcription factor 3
F: POU class 2 homeobox associating factor 3
G: DNA containing POU domain recognition element octamer (sense strand)
H: DNA containing POU domain recognition element octamer (antisense strand)


Theoretical massNumber of molelcules
Total (without water)63,7968
Polymers63,7968
Non-polymers00
Water1086
1
A: POU domain, class 2, transcription factor 3
B: POU class 2 homeobox associating factor 3
C: DNA containing POU domain recognition element octamer (sense strand)
D: DNA containing POU domain recognition element octamer (antisense strand)


Theoretical massNumber of molelcules
Total (without water)31,8984
Polymers31,8984
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-41 kcal/mol
Surface area13610 Å2
MethodPISA
2
E: POU domain, class 2, transcription factor 3
F: POU class 2 homeobox associating factor 3
G: DNA containing POU domain recognition element octamer (sense strand)
H: DNA containing POU domain recognition element octamer (antisense strand)


Theoretical massNumber of molelcules
Total (without water)31,8984
Polymers31,8984
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-40 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.165, 36.022, 88.598
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein POU domain, class 2, transcription factor 3 / Octamer-binding protein 11 / Oct-11 / Octamer-binding transcription factor 11 / OTF-11 / ...Octamer-binding protein 11 / Oct-11 / Octamer-binding transcription factor 11 / OTF-11 / Transcription factor PLA-1 / Transcription factor Skn-1


Mass: 18503.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POU2F3, OTF11, PLA1 / Plasmid: pHIS-Parallel-GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q9UKI9
#2: Protein/peptide POU class 2 homeobox associating factor 3 / Cancer susceptibility candidate protein 13 / Colorectal cancer-associated protein 2 / Protein OCA-T2


Mass: 4218.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POU2AF3, C11orf93, CASC13, COLCA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A8K830
#3: DNA chain DNA containing POU domain recognition element octamer (sense strand)


Mass: 4657.060 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA containing POU domain recognition element octamer (antisense strand)


Mass: 4518.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M MIB (2:3:3 molar ratio of malonate:imidazole:boric acid), pH 4.0, 25% PEG-1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979493 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 2.79→38.91 Å / Num. obs: 13089 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.064 / Rrim(I) all: 0.119 / Χ2: 0.96 / Net I/σ(I): 6.8 / Num. measured all: 44150
Reflection shellResolution: 2.79→2.94 Å / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.759 / Num. measured all: 5884 / Num. unique obs: 1765 / CC1/2: 0.719 / Rpim(I) all: 0.483 / Rrim(I) all: 0.902 / Χ2: 1.08 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
XDSFebruary 5, 2021data reduction
pointless1.12.10data scaling
Aimless0.7.7data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.19.2_4158refinement
MolProbitymodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→38.91 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 661 5.11 %
Rwork0.2358 --
obs0.2385 12932 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 1218 0 6 3919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034093
X-RAY DIFFRACTIONf_angle_d0.6425731
X-RAY DIFFRACTIONf_dihedral_angle_d21.5831684
X-RAY DIFFRACTIONf_chiral_restr0.04631
X-RAY DIFFRACTIONf_plane_restr0.004523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-30.44181240.37652374X-RAY DIFFRACTION96
3.01-3.310.33711300.31122369X-RAY DIFFRACTION97
3.31-3.790.33591290.24072420X-RAY DIFFRACTION98
3.79-4.770.25871350.22092508X-RAY DIFFRACTION100
4.77-38.910.27031430.20492600X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.91091.6104-0.02014.9153-0.38183.88570.7477-0.74420.23050.2665-0.4415-0.3656-0.20470.5301-0.1730.715-0.1196-0.01260.59660.00570.814436.36952.010620.0595
25.1973-0.75050.07043.0491-2.69082.89570.0736-0.23230.64030.1472-0.1792-0.4898-0.08990.3502-0.00620.6638-0.04970.03670.44270.10010.841736.53262.311317.2475
36.0426-0.5603-1.22643.30971.18583.1444-0.29580.6517-2.05630.78150.11180.77571.2118-0.71220.04540.90360.12290.0130.78670.07451.159518.6772-13.08547.5598
40.1996-0.971-0.05284.76040.17433.8773-1.2049-0.1353-1.1890.1213-0.0689-1.42930.82160.85211.02851.03380.1090.22930.50080.19111.562540.7983-20.047810.5343
52.8853-0.57120.20724.406-1.56545.82830.53721.04320.4335-0.4305-0.1832-0.03850.0584-0.9555-0.30780.48380.0678-0.01420.7670.17430.670622.3258-0.07457.5013
63.64720.77980.8943.74612.01292.85010.3210.4160.121-0.29450.44140.394-0.1115-1.1487-0.8440.67940.1543-0.02590.82540.28020.646420.16960.32814.4001
72.18520.0522-0.07092.4540.1422.6034-0.215-0.31460.17390.13520.04771.40240.9413-0.38890.41351.4880.13390.50551.40640.46511.63082.2661-22.0648-28.7844
81.42850.58990.45770.43450.26780.3787-0.0180.8163-0.1120.1703-0.19520.76590.1326-0.35170.12280.78210.05780.19581.30320.27481.16813.3646-18.8017-31.1187
92.042.02530.77083.64521.37832.92210.2807-0.31560.69361.4044-0.06090.001-0.31111.0483-0.35261.25920.0876-0.14441.1460.13290.872519.4995-4.5471-28.2477
100.3695-0.7635-1.14463.89623.30753.9809-0.5998-0.05940.36251.13090.14470.3990.18751.51260.52891.52540.3064-0.15321.37390.11830.95872.785-3.1063-19.9371
113.7982-0.0181-1.65352.9811.22052.79030.0781-0.4101-0.34920.68220.24870.52420.20740.2324-0.36160.75230.17740.11280.92150.24630.649717.6302-13.7926-35.3002
122.8221-0.0179-0.70383.19790.29141.3537-0.3777-0.7798-0.67180.83410.2723-0.17090.1990.54580.12480.74850.10440.04590.8310.19240.600620.02-12.0645-37.7972
135.7386-0.0264-0.75383.91922.21323.2450.71420.76870.0971-0.2883-0.52970.4066-0.426-1.6783-0.21450.99910.1622-0.00461.62010.30750.86979.58344.0551-1.6489
145.4504-1.3027-1.51985.22240.86144.1851-0.1604-0.9538-0.25210.38250.2076-0.46130.40641.158-0.10760.70990.0692-0.08041.10580.18420.599530.8103-11.2073-44.5564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 185 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 262 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 16 )
4X-RAY DIFFRACTION4chain 'B' and (resid 17 through 34 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 15 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 15 )
7X-RAY DIFFRACTION7chain 'E' and (resid 184 through 225 )
8X-RAY DIFFRACTION8chain 'E' and (resid 226 through 257 )
9X-RAY DIFFRACTION9chain 'F' and (resid 6 through 16 )
10X-RAY DIFFRACTION10chain 'F' and (resid 17 through 27 )
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 15 )
12X-RAY DIFFRACTION12chain 'H' and (resid 1 through 15 )
13X-RAY DIFFRACTION13chain 'A' and (resid 281 through 341 )
14X-RAY DIFFRACTION14chain 'E' and (resid 281 through 341 )

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