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- PDB-1hf0: Crystal structure of the DNA-binding domain of Oct-1 bound to DNA... -

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Basic information

Entry
Database: PDB / ID: 1hf0
TitleCrystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer
Components
  • DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3'
  • DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3'
  • OCTAMER-BINDING TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION / OCT-1 / POU DOMAIN / DIMER
Function / homology
Function and homology information


RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / sequence-specific DNA binding ...RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
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 / 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 ...POU domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / Octamer-binding 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 / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / 434 Repressor (Amino-terminal Domain) / 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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsRemenyi, A. / Tomilin, A. / Pohl, E. / Scholer, H.R. / Wilmanns, M.
CitationJournal: Mol.Cell / Year: 2001
Title: Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping
Authors: Remenyi, A. / Tomilin, A. / Pohl, E. / Lins, K. / Philippsen, A. / Reinbold, R. / Scholer, H.R. / Wilmanns, M.
History
DepositionNov 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2001Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
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

Downloads & links

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Assembly

Deposited unit
A: OCTAMER-BINDING TRANSCRIPTION FACTOR 1
B: OCTAMER-BINDING TRANSCRIPTION FACTOR 1
M: DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3'
N: DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)50,1574
Polymers50,1574
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-36 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.250, 131.250, 116.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein OCTAMER-BINDING TRANSCRIPTION FACTOR 1


Mass: 18327.795 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organelle: NUCLEUS / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14859
#2: DNA chain DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3'


Mass: 6833.456 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3'


Mass: 6668.313 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.3 / Details: pH 5.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8856, 0.9185, 0.9190, 0.8424
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
20.91851
30.9191
40.84241
ReflectionResolution: 2.7→20 Å / Num. obs: 16742 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 23
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.389 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2941 818 5 %RANDOM
Rwork0.2391 ---
obs0.2391 16742 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 896 0 119 3079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.4
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: 2.7→2.76 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.4312 33 4 %
Rwork0.3719 975 -

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