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- PDB-6ht5: Oct4/Sox2:UTF1 structure -

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Basic information

Entry
Database: PDB / ID: 6ht5
TitleOct4/Sox2:UTF1 structure
Components
  • DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')
  • POU domain, class 5, transcription factor 1
  • Transcription factor SOX-2
KeywordsTRANSCRIPTION / Cell reprogramming / transcription factor / DNA binding
Function / homology
Function and homology information


diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / ectodermal cell fate commitment / response to benzoic acid / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception ...diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / ectodermal cell fate commitment / response to benzoic acid / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / trophectodermal cell fate commitment / forebrain neuron differentiation / blastocyst growth / anatomical structure formation involved in morphogenesis / positive regulation of epithelial cell differentiation / regulation of asymmetric cell division / endodermal cell fate specification / response to oxygen-glucose deprivation / adenohypophysis development / Deactivation of the beta-catenin transactivating complex / endodermal cell fate commitment / germ-line stem cell population maintenance / POU domain binding / positive regulation of cell-cell adhesion / detection of mechanical stimulus involved in sensory perception of sound / neuron fate commitment / negative regulation of calcium ion-dependent exocytosis / trophectodermal cell differentiation / neuronal stem cell population maintenance / male genitalia development / female germ cell nucleus / germ cell nucleus / cell fate specification / inner ear morphogenesis / tongue development / lung alveolus development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell population maintenance / epithelial tube branching involved in lung morphogenesis / positive regulation of Notch signaling pathway / positive regulation of neuroblast proliferation / negative regulation of Wnt signaling pathway / cytokine binding / inner ear development / somatic stem cell population maintenance / negative regulation of cell differentiation / blastocyst development / regulation of neurogenesis / negative regulation of neuron differentiation / cell fate commitment / neuroblast proliferation / embryonic organ development / positive regulation of transcription initiation by RNA polymerase II / negative regulation of osteoblast differentiation / cis-regulatory region sequence-specific DNA binding / response to retinoic acid / forebrain development / Notch signaling pathway / transcription repressor complex / positive regulation of neuron differentiation / cellular response to cadmium ion / male germ cell nucleus / cellular response to leukemia inhibitory factor / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / lysine-acetylated histone binding / brain development / negative regulation of canonical Wnt signaling pathway / neuron differentiation / chromatin DNA binding / cerebral cortex development / Wnt signaling pathway / osteoblast differentiation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm
Similarity search - Function
Transcription factor SOX / SOX 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 ...Transcription factor SOX / SOX 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 / : / High mobility group box domain / DNA Binding (I), subunit A / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / 434 Repressor (Amino-terminal Domain) / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / POU domain, class 5, transcription factor 1 / Transcription factor SOX-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.451 Å
AuthorsVahokoski, J. / Meusch, D. / Groves, M. / Pogenberg, V. / Wilmanns, M.
CitationJournal: To Be Published
Title: Oct4/Sox2:UTF1 structure
Authors: Vahokoski, J. / Pogenberg, V. / Wilmanns, M.
History
DepositionOct 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')
B: DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')
D: Transcription factor SOX-2
E: POU domain, class 5, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)41,1374
Polymers41,1374
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-27 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.170, 165.170, 39.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: DNA chain DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')


Mass: 6757.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: DNA chain DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')


Mass: 6455.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Protein Transcription factor SOX-2


Mass: 10092.858 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox2, Sox-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P48432
#4: Protein POU domain, class 5, transcription factor 1 / NF-A3 / Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding ...NF-A3 / Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding transcription factor 3 / OTF-3


Mass: 17831.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pou5f1, Oct-3, Oct-4, Otf-3, Otf3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20263

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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: 3.8 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM 4-morpholineethanesulfonic acid at pH 6.0, 33% v/v 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.45→48.62 Å / Num. obs: 8480 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.5
Reflection shellResolution: 3.45→3.6 Å / Rmerge(I) obs: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O4X

1o4x


Resolution: 3.451→47.68 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 683 8.06 %
Rwork0.2011 --
obs0.205 8479 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.451→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 879 0 0 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042415
X-RAY DIFFRACTIONf_angle_d0.6473438
X-RAY DIFFRACTIONf_dihedral_angle_d21.6491313
X-RAY DIFFRACTIONf_chiral_restr0.034383
X-RAY DIFFRACTIONf_plane_restr0.003291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4515-3.71790.34851340.27431523X-RAY DIFFRACTION100
3.7179-4.09180.30471340.23311543X-RAY DIFFRACTION100
4.0918-4.68350.25311370.19521544X-RAY DIFFRACTION100
4.6835-5.8990.29121360.2081568X-RAY DIFFRACTION100
5.899-47.6850.19351420.17421618X-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)
16.3861-2.218-5.51550.95132.13875.3647-0.09121.4253-1.83313.9639-0.03890.40574.793-2.05660.29882.2741-0.0536-0.24591.34380.15812.518632.43450.53462.09
26.49222.0418-0.27824.0871-3.26155.37241.0568-0.3507-0.28250.539-0.43261.49361.60290.0744-0.66331.3794-0.02150.14610.9764-0.05831.329717.027462.57896.065
36.64412.0084-1.49759.0570.7928.6353-0.98990.5013-0.71761.9475-0.80842.12691.9573-0.35671.63311.7372-0.14660.4942.0629-0.09952.8153-11.117160.469812.9915
45.1738-4.27270.15553.73610.43131.90230.27291.5947-2.742-2.151-0.8430.97060.44430.60690.16141.8187-0.0456-0.02611.4162-0.29153.1678-10.074354.68129.7545
53.31.9095-1.54143.80880.42294.7688-0.7152-1.1942-1.67780.68270.0994-0.28861.1340.5740.53141.34710.27470.05951.26260.03441.481323.376859.14244.4679
63.84140.65680.15056.6216-0.87035.51771.41211.527-1.0291-0.2938-0.6969-1.06750.79780.978-0.66351.06260.06410.13821.0924-0.1740.953737.944665.24330.4146
77.81283.84982.74145.40355.21365.15520.43470.2434-1.78872.41820.8571-0.56570.8810.7324-0.0921.87410.2347-0.1191.10380.21330.172237.427367.290111.22
86.46193.52495.64035.05912.63475.0514-1.04781.17821.9575-0.2315-1.15060.0412-0.33810.58991.3171.07790.26260.18341.1042-0.03090.763728.747377.3869-1.9889
97.5677-0.98624.38495.1533-3.98434.86440.38441.7193-1.1176-1.80930.11251.98721.33420.1789-0.14351.02020.06990.10421.2864-0.21871.197317.679661.1913-6.226
103.8077-2.7813.05293.49860.1495.43331.49721.97780.3761-0.6779-0.69230.30210.63540.0723-0.75060.87660.1140.10411.15380.16561.12585.48176.0006-9.9153
113.9857-3.3090.11385.2493-0.54662.3547-0.0065-0.35411.12340.35960.18180.0499-0.29390.3505-0.33880.81860.04270.04360.8871-0.24111.021814.348883.86850.1838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 3 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 13 )
3X-RAY DIFFRACTION3chain 'A' and (resid 14 through 20 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 4 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 20 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 29 )
7X-RAY DIFFRACTION7chain 'D' and (resid 30 through 45 )
8X-RAY DIFFRACTION8chain 'D' and (resid 46 through 66 )
9X-RAY DIFFRACTION9chain 'D' and (resid 67 through 77 )
10X-RAY DIFFRACTION10chain 'E' and (resid -1 through 23 )
11X-RAY DIFFRACTION11chain 'E' and (resid 24 through 99 )

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