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- PDB-8bx1: Oct4/Sox2 protein:DNA complex -

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Basic information

Entry
Database: PDB / ID: 8bx1
TitleOct4/Sox2 protein:DNA complex
Components
  • HOXB1_f
  • HOXB1_r
  • POU domain, class 5, transcription factor 1
  • Transcription factor SOX-2
KeywordsTRANSCRIPTION / Oct4 / Sox2 / Hoxb1
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 / anatomical structure formation involved in morphogenesis / regulation of asymmetric cell division / endodermal cell fate specification / positive regulation of epithelial cell differentiation / adenohypophysis development / tongue development / Deactivation of the beta-catenin transactivating complex / blastocyst growth / POU domain binding / endodermal cell fate commitment / germ-line stem cell population maintenance / neuron fate commitment / neuronal stem cell population maintenance / negative regulation of calcium ion-dependent exocytosis / trophectodermal cell differentiation / detection of mechanical stimulus involved in sensory perception of sound / male genitalia development / female germ cell nucleus / cell fate specification / germ cell nucleus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / inner ear morphogenesis / lung alveolus development / stem cell population maintenance / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / positive regulation of Notch signaling pathway / epithelial tube branching involved in lung morphogenesis / cytokine binding / cellular response to cadmium ion / negative regulation of Wnt signaling pathway / blastocyst development / somatic stem cell population maintenance / negative regulation of cell differentiation / neuroblast proliferation / cell fate commitment / embryonic organ development / regulation of neurogenesis / positive regulation of transcription initiation by RNA polymerase II / response to retinoic acid / negative regulation of osteoblast differentiation / cis-regulatory region sequence-specific DNA binding / : / Notch signaling pathway / transcription repressor complex / positive regulation of neuron differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / telomere maintenance / cellular response to leukemia inhibitory factor / male germ cell nucleus / stem cell differentiation / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / cerebral cortex development / chromatin DNA binding / Wnt signaling pathway / nuclear receptor activity / neuron differentiation / osteoblast differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / sequence-specific DNA binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor 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 / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / 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: 2.5 Å
AuthorsChojnowski, G. / Wilmanns, M. / Round, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Oct4-Soc2-HoxB1 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
D: HOXB1_r
C: HOXB1_f
A: POU domain, class 5, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)41,5564
Polymers41,5564
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-39 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.199, 65.892, 126.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: DNA chain HOXB1_r


Mass: 6752.419 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)
#3: DNA chain HOXB1_f


Mass: 6747.374 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: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M sodium acetate, 12% (v/v) PEG 4000

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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: Jun 8, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.5→126.92 Å / Num. obs: 15480 / % possible obs: 99.7 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 2 / Num. unique obs: 1711 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ht5

6ht5


Resolution: 2.5→58.48 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.916 / SU B: 26.716 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 747 4.8 %RANDOM
Rwork0.25311 ---
obs0.25414 14681 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---2.88 Å20 Å2
3---3.04 Å2
Refinement stepCycle: 1 / Resolution: 2.5→58.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 861 0 4 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3751.7073757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94420.30399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96615345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7541519
X-RAY DIFFRACTIONr_chiral_restr0.1580.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021682
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_it4.4135.66811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.9068.4661007
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6835.9151854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.13710792
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 61 -
Rwork0.403 1065 -
obs--99.56 %
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)
10.9038-0.456-0.11972.66750.10430.67610.09210.0902-0.11260.1204-0.13150.15990.0751-0.00290.03940.103-0.0188-0.00750.0564-0.01790.065-0.7674-16.0785-11.9833
20.184-0.27910.01964.7917-1.32130.5790.15120.03870.078-0.0888-0.1796-0.36070.01520.1410.02840.13920.04110.03750.09070.0360.128812.49830.2394-17.4779
30.84861.421-0.87172.652-1.35211.02470.1738-0.02270.04010.1684-0.20210.0156-0.16980.0070.02840.13510.06390.02030.16690.13760.199712.22691.4926-18.377
40.62090.3122-0.30420.62690.03290.93880.30960.34120.23940.3194-0.02980.05850.0329-0.0995-0.27970.23380.12770.07580.30150.13050.15388.846311.3465-22.1965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 77
2X-RAY DIFFRACTION2D2 - 22
3X-RAY DIFFRACTION3C2 - 22
4X-RAY DIFFRACTION4A-2 - 149

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