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- PDB-8t0f: Crystal structure of the PEG10 promoter-bound ONECUT2 DNA-binding... -

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Basic information

Entry
Database: PDB / ID: 8t0f
TitleCrystal structure of the PEG10 promoter-bound ONECUT2 DNA-binding domain
Components
  • DNA (5'-D(P*AP*GP*AP*TP*CP*GP*AP*TP*TP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*AP*AP*TP*CP*GP*AP*TP*CP*T)-3')
  • One cut domain family member 2
KeywordsTRANSCRIPTION/DNA / ONECUT family Transcription factor CUT-Homeodomain Prostate cancer DNA-binding / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


mesenchymal stem cell migration / peripheral nervous system neuron development / positive regulation of mesenchymal stem cell migration / regulation of cell-matrix adhesion / endocrine pancreas development / epithelial cell development / cilium assembly / cell fate commitment / transforming growth factor beta receptor signaling pathway / liver development ...mesenchymal stem cell migration / peripheral nervous system neuron development / positive regulation of mesenchymal stem cell migration / regulation of cell-matrix adhesion / endocrine pancreas development / epithelial cell development / cilium assembly / cell fate commitment / transforming growth factor beta receptor signaling pathway / liver development / animal organ morphogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / sequence-specific double-stranded DNA binding / actin cytoskeleton / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / CUT domain / CUT domain / CUT domain profile. / CUT / 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) / One cut domain family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsChatterjee, A. / Katiki, M. / Murali, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)PC210486 United States
CitationJournal: Nat Commun / Year: 2024
Title: The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.
Authors: Chatterjee, A. / Gallent, B. / Katiki, M. / Qian, C. / Harter, M.R. / Silletti, S. / Komives, E.A. / Freeman, M.R. / Murali, R.
History
DepositionMay 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: One cut domain family member 2
B: DNA (5'-D(P*AP*GP*AP*TP*CP*GP*AP*TP*TP*TP*GP*C)-3')
C: DNA (5'-D(P*GP*CP*AP*AP*AP*TP*CP*GP*AP*TP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)26,0183
Polymers26,0183
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-25 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.229, 78.303, 39.447
Angle α, β, γ (deg.)90.00, 110.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

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Components

#1: Protein One cut domain family member 2 / Hepatocyte nuclear factor 6-beta / HNF-6-beta / One cut homeobox 2 / Transcription factor ONECUT-2 / OC-2


Mass: 18693.707 Da / Num. of mol.: 1 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ONECUT2, HNF6B / Plasmid: pET His6 TEV LIC vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95948
#2: DNA chain DNA (5'-D(P*AP*GP*AP*TP*CP*GP*AP*TP*TP*TP*GP*C)-3')


Mass: 3677.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*GP*CP*AP*AP*AP*TP*CP*GP*AP*TP*CP*T)-3')


Mass: 3646.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.04 M KH2PO4, 16 % PEG 8000 and 20 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 8330 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.2 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.048 / Rrim(I) all: 0.13 / Χ2: 2.956 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.647.31.2924330.7030.9090.5071.3892.11798.4
2.64-2.697.41.0453850.7710.9330.4081.1232.26398.2
2.69-2.747.41.0583970.7710.9330.4131.1362.36598.5
2.74-2.87.40.8494280.820.9490.3320.9122.40698.4
2.8-2.867.30.9374030.8030.9440.3681.0072.39798.5
2.86-2.937.30.7814260.8480.9580.3060.8392.41199.1
2.93-37.30.6314070.8990.9730.2490.6782.5998.5
3-3.087.40.5634080.9260.980.2210.6052.76599
3.08-3.177.40.264150.9930.9980.1020.282.7798.8
3.17-3.287.40.068413110.0270.0732.95799
3.28-3.397.40.2424080.9790.9950.0950.2613.27299.5
3.39-3.537.40.1424270.9940.9990.0560.1523.36299.3
3.53-3.697.30.1274090.9930.9980.050.1363.60899.5
3.69-3.887.30.1124290.9950.9990.0440.123.67999.8
3.88-4.137.30.1014200.9940.9990.040.1093.63699.8
4.13-4.457.10.0794110.9960.9990.0310.0853.68299.5
4.45-4.897.30.0734330.9980.9990.0290.0793.441100
4.89-5.67.40.0714250.9980.9990.0280.0763.314100
5.6-7.057.30.0634180.9980.9990.0250.0683.048100
7.05-507.20.0394350.99910.0160.0422.97898.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
HKL-2000v721.3data scaling
HKL-2000v721.3data reduction
MOLREP11.7.03; 13.07.2020phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→29.51 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 431 5.2 %
Rwork0.2278 --
obs0.2306 8283 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 492 0 37 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031709
X-RAY DIFFRACTIONf_angle_d0.6032396
X-RAY DIFFRACTIONf_dihedral_angle_d27.623385
X-RAY DIFFRACTIONf_chiral_restr0.036264
X-RAY DIFFRACTIONf_plane_restr0.005220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.980.44371690.34432543X-RAY DIFFRACTION97
2.98-3.760.32751160.24042617X-RAY DIFFRACTION98
3.76-29.510.22321460.19342692X-RAY DIFFRACTION100

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