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- PDB-9pfp: Structure of POU2F3 POU domains bound to coactivator OCA-T1 and DNA -

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Basic information

Entry
Database: PDB / ID: 9pfp
TitleStructure of POU2F3 POU domains bound to coactivator OCA-T1 and DNA
Components
  • (DNA containing POU domain recognition element octamer ...) x 2
  • POU domain class 2-associating factor 2
  • 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 / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein POU2AF2 / POU domain class 2-associating factor 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. ...Protein POU2AF2 / POU domain class 2-associating factor 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
BORIC ACID / DNA / DNA (> 10) / POU domain class 2-associating factor 2 / POU domain, class 2, transcription factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 domain class 2-associating factor 2
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 domain class 2-associating factor 2
G: DNA containing POU domain recognition element octamer (sense strand)
H: DNA containing POU domain recognition element octamer (antisense strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,55411
Polymers64,3688
Non-polymers1853
Water5,350297
1
A: POU domain, class 2, transcription factor 3
B: POU domain class 2-associating factor 2
C: DNA containing POU domain recognition element octamer (sense strand)
D: DNA containing POU domain recognition element octamer (antisense strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3086
Polymers32,1844
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-37 kcal/mol
Surface area12390 Å2
MethodPISA
2
E: POU domain, class 2, transcription factor 3
F: POU domain class 2-associating factor 2
G: DNA containing POU domain recognition element octamer (sense strand)
H: DNA containing POU domain recognition element octamer (antisense strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2465
Polymers32,1844
Non-polymers621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-42 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.785, 94.260, 56.801
Angle α, β, γ (deg.)90.00, 115.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA containing POU domain recognition element octamer ... , 2 types, 4 molecules CGDH

#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)

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Protein / Protein/peptide , 2 types, 4 molecules AEBF

#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 domain class 2-associating factor 2 / Oct coactivator from tuft cells 1 / Protein OCA-T1 / POU class 2 homeobox-associating factor 2


Mass: 4504.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POU2AF2, C11orf53 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q8IXP5

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Non-polymers , 2 types, 300 molecules

#5: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BH3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.88 Å3/Da / Density % sol: 34.43 % / Description: Rod-shaped or planar
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: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→34.76 Å / Num. obs: 51249 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.025 / Rrim(I) all: 0.047 / Χ2: 0.93 / Net I/σ(I): 13.6 / Num. measured all: 177735
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.904 / Num. unique obs: 2642 / CC1/2: 0.713 / Rpim(I) all: 0.591 / Rrim(I) all: 1.085 / Χ2: 0.88 / % possible all: 96

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Processing

Software
NameVersionClassification
XDSJanuary 10, 2022data reduction
pointless1.12.13data scaling
Aimless0.7.8data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20.1_4487refinement
MolProbitymodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.76 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 2549 4.98 %
Rwork0.1751 --
obs0.1765 51157 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 1218 12 297 4085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073988
X-RAY DIFFRACTIONf_angle_d0.9325586
X-RAY DIFFRACTIONf_dihedral_angle_d21.5581639
X-RAY DIFFRACTIONf_chiral_restr0.048613
X-RAY DIFFRACTIONf_plane_restr0.009502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.24031350.26562631X-RAY DIFFRACTION96
1.74-1.770.30541390.252690X-RAY DIFFRACTION98
1.77-1.810.2611520.24212619X-RAY DIFFRACTION98
1.81-1.850.28591460.24022703X-RAY DIFFRACTION99
1.85-1.90.26211400.24392724X-RAY DIFFRACTION100
1.9-1.950.31371500.2572671X-RAY DIFFRACTION99
1.95-2.010.26931740.23852718X-RAY DIFFRACTION100
2.01-2.070.31151450.20762701X-RAY DIFFRACTION99
2.07-2.150.23191220.19612714X-RAY DIFFRACTION99
2.15-2.230.25331320.19352697X-RAY DIFFRACTION99
2.23-2.330.24471520.20172701X-RAY DIFFRACTION99
2.33-2.460.21651380.18092703X-RAY DIFFRACTION99
2.46-2.610.25011370.18482688X-RAY DIFFRACTION98
2.61-2.810.21171650.18732673X-RAY DIFFRACTION99
2.81-3.10.25111400.19692753X-RAY DIFFRACTION100
3.1-3.540.18911350.16212709X-RAY DIFFRACTION98
3.54-4.460.16221350.13972729X-RAY DIFFRACTION99
4.46-34.760.13821120.15232784X-RAY DIFFRACTION99
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)
11.64780.07210.06654.9236-2.59685.28880.0019-0.4780.08850.58310.0347-0.07-0.37460.23040.03080.430.0008-0.09750.3411-0.03050.487220.1017-0.2188-11.2523
25.2248-0.950.11146.22041.29765.0485-0.09490.05420.5315-0.3441-0.0262-1.1427-0.8060.84290.10940.4037-0.06050.03740.50540.08150.484527.667-2.7686-20.3889
35.2827-0.52380.70293.98591.2992.0324-0.0212-0.31550.26950.1026-0.06530.0197-0.144-0.08610.12130.29710.0411-0.0220.3004-0.020.272514.1984-7.4433-15.2986
47.62372.01532.61221.18551.14414.7788-0.0676-0.7195-1.07690.48970.0119-0.00230.3593-0.90910.00030.4931-0.03240.09790.4459-0.00110.36872.202-18.2928-15.1804
53.1031-0.63460.16381.33980.01240.72010.4178-0.2442-0.60860.5586-0.66931.46760.3922-0.62610.11280.6127-0.030.30590.8747-0.23760.9394-14.489-22.071-21.8026
62.31821.35980.84862.32751.59382.8168-0.1065-0.03180.19610.1051-0.12630.10350.0359-0.26730.22870.24460.00340.01350.2440.01630.21827.5991-15.317-24.8124
71.61440.11750.20192.13981.90373.0668-0.0483-0.02130.01040.0057-0.186-0.00830.0754-0.13750.23450.29730.01420.00240.29140.00870.30189.4868-12.933-22.6245
82.68330.8013-0.52132.8145-1.43643.01360.1741-0.1997-0.27890.3044-0.3191-0.47240.12580.56160.13120.34440.0103-0.050.40160.06360.378715.796111.67445.1796
94.92251.11431.31541.99280.57432.5509-0.0210.31720.1002-0.07550.0448-0.12040.04520.0494-0.02030.22590.01460.01120.21780.02710.2195-11.031-4.9358-4.2229
104.07081.05190.75262.6018-0.04832.41380.174-0.9860.02720.3457-0.33830.8677-0.2969-0.890.16970.3892-0.02150.04340.5129-0.06370.4713-6.00237.135211.9418
113.28210.2270.35793.44090.56416.6605-0.0802-1.31780.15191.17480.30450.3848-0.2283-0.7779-0.170.60190.0320.07280.79180.07260.41467.449812.22923.0402
121.61471.9103-0.04873.44450.47030.7690.1582-0.0293-0.07790.146-0.1986-0.01760.08640.10150.04740.28640.018-0.01560.3001-0.00150.26210.31834.1022.8166
131.79891.344-0.22982.5961-0.27120.67820.0918-0.0535-0.15330.0392-0.2067-0.12860.12190.03160.10680.3160.0081-0.01720.3509-0.02170.2638-2.19841.32092.3357
143.838-2.3493-0.73344.41110.25792.1470.03740.0593-0.7142-0.0642-0.59061.9130.0623-1.06010.51760.3237-0.10820.01650.6635-0.19780.6802-9.0852-25.2513-36.6787
150.97130.9941-0.72493.6024-1.50921.9916-0.16490.0624-0.2953-0.1675-0.1627-0.03480.147-0.17290.35760.3224-0.03440.04330.3147-0.0120.33645.3813-23.637-42.5261
165.241.0247-1.71792.28121.63992.4546-0.05950.60560.8111-0.7381-0.3784-0.2844-1.2665-1.25340.42770.58220.06690.02470.40490.00840.37076.484-16.3456-38.1309
173.0596-0.8198-0.40962.15080.3881.8116-0.1656-0.5298-0.21570.5679-0.1860.45510.2377-0.50090.34230.3413-0.05670.07230.3699-0.06740.3178-0.3034-22.375-29.7282
183.3167-0.811-1.37654.00573.40848.2572-0.1440.58230.4989-0.5445-0.61760.4224-1.0178-0.91640.74960.28210.0504-0.02070.584-0.10320.4827-4.6963-16.8628-38.4577
192.88721.15041.72510.96381.12783.1455-0.34540.6282-0.09280.15140.26730.2068-0.22210.36680.00410.5668-0.06130.01020.42250.01170.475912.5369-15.118-32.4968
203.9138-1.4555-1.05373.97991.64516.0325-0.2517-0.2623-0.47230.01880.02330.28720.63280.62990.16710.32630.07080.01390.42920.09510.394224.1886-12.1654-12.4482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 303 through 307 )
2X-RAY DIFFRACTION2chain 'E' and (resid 308 through 321 )
3X-RAY DIFFRACTION3chain 'E' and (resid 322 through 340 )
4X-RAY DIFFRACTION4chain 'F' and (resid 11 through 21 )
5X-RAY DIFFRACTION5chain 'F' and (resid 22 through 32 )
6X-RAY DIFFRACTION6chain 'G' and (resid 1 through 15 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 15 )
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 257 )
9X-RAY DIFFRACTION9chain 'A' and (resid 258 through 340 )
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 21 )
11X-RAY DIFFRACTION11chain 'B' and (resid 22 through 32 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 15 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 15 )
14X-RAY DIFFRACTION14chain 'E' and (resid 186 through 204 )
15X-RAY DIFFRACTION15chain 'E' and (resid 205 through 220 )
16X-RAY DIFFRACTION16chain 'E' and (resid 221 through 225 )
17X-RAY DIFFRACTION17chain 'E' and (resid 226 through 238 )
18X-RAY DIFFRACTION18chain 'E' and (resid 239 through 256 )
19X-RAY DIFFRACTION19chain 'E' and (resid 257 through 289 )
20X-RAY DIFFRACTION20chain 'E' and (resid 290 through 302 )

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