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- PDB-1gt0: Crystal structure of a POU/HMG/DNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 1gt0
TitleCrystal structure of a POU/HMG/DNA ternary complex
Components
  • 5'-D(*AP*TP*CP*CP*CP*AP*TP*TP*AP*GP* CP*AP*TP*CP*CP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'
  • 5'-D(*TP*TP*CP*TP*TP*TP*GP*TP*TP*TP* GP*GP*AP* TP*GP*CP*TP*AP*AP*TP*GP*GP*GP*A)-3'
  • OCTAMER-BINDING TRANSCRIPTION FACTOR 1
  • TRANSCRIPTION FACTOR SOX-2
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / POU FACTORS / SOX PROTEINS
Function / homology
Function and homology information


diencephalon morphogenesis / regulation of myofibroblast cell apoptotic process / olfactory placode formation / lens induction in camera-type eye / response to oxygen-glucose deprivation / retina morphogenesis in camera-type eye / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / adenohypophysis development / anatomical structure formation involved in morphogenesis ...diencephalon morphogenesis / regulation of myofibroblast cell apoptotic process / olfactory placode formation / lens induction in camera-type eye / response to oxygen-glucose deprivation / retina morphogenesis in camera-type eye / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / adenohypophysis development / anatomical structure formation involved in morphogenesis / forebrain neuron differentiation / positive regulation of epithelial cell differentiation / endodermal cell fate specification / epithelial tube branching involved in lung morphogenesis / tongue development / Deactivation of the beta-catenin transactivating complex / negative regulation of cell cycle G1/S phase transition / neuronal stem cell population maintenance / positive regulation of cell-cell adhesion / male genitalia development / neuron fate commitment / detection of mechanical stimulus involved in sensory perception of sound / lung alveolus development / response to growth factor / cell fate specification / somatic stem cell population maintenance / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / inner ear morphogenesis / forebrain development / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / miRNA binding / embryonic organ development / stem cell population maintenance / positive regulation of Notch signaling pathway / inner ear development / cellular response to cadmium ion / cell fate commitment / negative regulation of cell differentiation / nitric-oxide synthase binding / negative regulation of Wnt signaling pathway / RNA polymerase II transcribes snRNA genes / regulation of neurogenesis / response to retinoic acid / negative regulation of osteoblast differentiation / positive regulation of neuron differentiation / RNA polymerase II core promoter sequence-specific DNA binding / stem cell differentiation / sensory perception of sound / gene expression / brain development / RNA polymerase II transcription regulator complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / cerebral cortex development / chromatin DNA binding / positive regulation of miRNA transcription / osteoblast differentiation / regulation of gene expression / neuron differentiation / transcription regulator complex / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
POU domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / Octamer-binding transcription factor / 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 domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / Octamer-binding transcription factor / 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. / lambda repressor-like DNA-binding domains / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / HMG (high mobility group) box / 434 Repressor (Amino-terminal Domain) / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / POU domain, class 2, transcription factor 1 / Transcription factor SOX-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsRemenyi, A. / Wilmanns, M.
CitationJournal: Genes Dev. / Year: 2003
Title: Crystal Structure of a POU/Hmg/DNA Ternary Complex Suggests Differential Assembly of Oct4 and Sox2 on Two Enhancers
Authors: Remenyi, A. / Lins, K. / Nissen, L.J. / Reinbold, R. / Scholer, H.R. / Wilmanns, M.
History
DepositionJan 9, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*TP*TP*CP*TP*TP*TP*GP*TP*TP*TP* GP*GP*AP* TP*GP*CP*TP*AP*AP*TP*GP*GP*GP*A)-3'
B: 5'-D(*AP*TP*CP*CP*CP*AP*TP*TP*AP*GP* CP*AP*TP*CP*CP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'
C: OCTAMER-BINDING TRANSCRIPTION FACTOR 1
D: TRANSCRIPTION FACTOR SOX-2


Theoretical massNumber of molelcules
Total (without water)42,8984
Polymers42,8984
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.800, 72.800, 172.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 7436.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FGF-4 ENHANCER / Source: (synth.) MUS MUSCULUS (house mouse)
#2: DNA chain 5'-D(*AP*TP*CP*CP*CP*AP*TP*TP*AP*GP* CP*AP*TP*CP*CP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'


Mass: 7299.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FGF-4 ENHANCER / Source: (synth.) MUS MUSCULUS (house mouse)
#3: Protein OCTAMER-BINDING TRANSCRIPTION FACTOR 1 / OTF-1 / NF-A1 / OCT-1


Mass: 18327.795 Da / Num. of mol.: 1 / Fragment: POU DOMAIN RESIDUES 280-438 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14859
#4: Protein TRANSCRIPTION FACTOR SOX-2


Mass: 9833.532 Da / Num. of mol.: 1 / Fragment: HMG DOMAIN RESIDUES 41-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET24-D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48432
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN C ENGINEERED MUTATION CYS340SER CYS428SER

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7
Details: 18% PEG3350, 50 MM HEPES PH 7.0, 20 MM MGCL2, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.846
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.846 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 16619 / % possible obs: 98.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 21.8
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.35 / % possible all: 96.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 836 5 %RANDOM
Rwork0.232 ---
obs0.232 16612 98.2 %-
Displacement parametersBiso mean: 58.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 978 0 90 2833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.66 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.4005 42 5 %
Rwork0.3935 858 -
obs--5.4 %

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