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- PDB-8bx2: Oct4/Sox2 protein:DNA complex -

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Basic information

Entry
Database: PDB / ID: 8bx2
TitleOct4/Sox2 protein:DNA complex
Components
  • POU domain, class 5, transcription factor 1
  • Transcription factor SOX-2
  • UTF1_f
  • UTF1_r
KeywordsTRANSCRIPTION / Oct4 / Sox2 / UTF1
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 / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process ...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 / 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 / regulation of asymmetric cell division / endodermal cell fate specification / blastocyst growth / adenohypophysis development / positive regulation of epithelial cell differentiation / Deactivation of the beta-catenin transactivating complex / anatomical structure formation involved in morphogenesis / endodermal cell fate commitment / POU domain binding / germ-line stem cell population maintenance / detection of mechanical stimulus involved in sensory perception of sound / neuron fate commitment / negative regulation of calcium ion-dependent exocytosis / neuronal stem cell population maintenance / trophectodermal cell differentiation / male genitalia development / female germ cell nucleus / cell fate specification / germ cell nucleus / tongue development / inner ear morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell population maintenance / positive regulation of Notch signaling pathway / positive regulation of neuroblast proliferation / lung alveolus development / cellular response to cadmium ion / epithelial tube branching involved in lung morphogenesis / negative regulation of Wnt signaling pathway / cytokine binding / somatic stem cell population maintenance / regulation of neurogenesis / blastocyst development / negative regulation of cell differentiation / neuroblast proliferation / negative regulation of neuron differentiation / cell fate commitment / positive regulation of transcription initiation by RNA polymerase II / negative regulation of osteoblast differentiation / embryonic organ development / cis-regulatory region sequence-specific DNA binding / response to retinoic acid / Notch signaling pathway / transcription repressor complex / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of neuron differentiation / cellular response to leukemia inhibitory factor / male germ cell nucleus / stem cell differentiation / lysine-acetylated histone binding / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / cerebral cortex development / neuron differentiation / chromatin DNA binding / Wnt signaling pathway / osteoblast differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / chromatin / 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 / nucleus / cytoplasm
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 / : / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / 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
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: 3.14 Å
AuthorsChojnowski, G. / Wilmanns, M. / Round, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Oct4-Soc2-UTF1 complex
Authors: Chojnowski, G. / Wilmanns, M. / Round, E.
History
DepositionDec 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Transcription factor SOX-2
A: POU domain, class 5, transcription factor 1
C: UTF1_r
D: UTF1_f


Theoretical massNumber of molelcules
Total (without water)41,5574
Polymers41,5574
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-31 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.169, 163.169, 39.792
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: 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
#2: 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: 17962.875 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
#3: DNA chain UTF1_r


Mass: 6781.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: DNA chain UTF1_f


Mass: 6719.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 70% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.137→81.585 Å / Num. obs: 8506 / % possible obs: 77.4 % / Redundancy: 19.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.8
Reflection shellResolution: 3.137→3.342 Å / Redundancy: 18.4 % / Rmerge(I) obs: 2.135 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 424 / CC1/2: 0.548 / % possible all: 22.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20200417data reduction
Aimless0.5.27data scaling
STARANISO2.3.28data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ht5

6ht5


Resolution: 3.14→81.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 20.584 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25234 368 4.3 %RANDOM
Rwork0.19861 ---
obs0.20075 8135 77.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.695 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20.75 Å20 Å2
2--1.5 Å2-0 Å2
3----4.86 Å2
Refinement stepCycle: 1 / Resolution: 3.14→81.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 902 0 0 2298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0112428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5081.7163459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.13320.48283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76415267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8781516
X-RAY DIFFRACTIONr_chiral_restr0.2190.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021512
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.12812.807700
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it19.05919.231870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it15.02715.6781728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined28.63510019
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.14→3.222 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 10 -
Rwork0.295 74 -
obs--10.4 %

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