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- PDB-1e3o: Crystal structure of Oct-1 POU dimer bound to MORE -

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Basic information

Entry
Database: PDB / ID: 1e3o
TitleCrystal structure of Oct-1 POU dimer bound to MORE
Components
  • 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3'
  • 5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*T)-3'
  • OCTAMER-BINDING TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION / POU DOMAIN / DIMER / DNA BINDING
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 / 'Homeobox' domain profile. / Homeodomain / lambda repressor-like DNA-binding domains / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRemenyi, A. / Tomilin, A. / Pohl, E. / Schoeler, H. / 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
DepositionJun 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2001Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: 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

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Assembly

Deposited unit
A: 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3'
B: 5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*T)-3'
C: OCTAMER-BINDING TRANSCRIPTION FACTOR 1


Theoretical massNumber of molelcules
Total (without water)25,1053
Polymers25,1053
Non-polymers00
Water2,486138
1
A: 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3'
B: 5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*T)-3'
C: OCTAMER-BINDING TRANSCRIPTION FACTOR 1

A: 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3'
B: 5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*T)-3'
C: OCTAMER-BINDING TRANSCRIPTION FACTOR 1


Theoretical massNumber of molelcules
Total (without water)50,2116
Polymers50,2116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area12540 Å2
ΔGint-5.9 kcal/mol
Surface area19660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)93.300, 52.400, 69.000
Angle α, β, γ (deg.)90.00, 127.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-211-

DA

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Components

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


Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain 5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*T)-3'


Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein OCTAMER-BINDING TRANSCRIPTION FACTOR 1


Mass: 18398.877 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THE PROTEIN WAS EXPRESSED IN E.COLI BY RECOMBINANT DNA TECHNOLOGY
Cellular location: NUCLEUSCell nucleus / Plasmid: PET-9D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14859
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN C ENGINEERED MUTATION CYS61SER CYS150SER

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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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growpH: 7 / Details: 22% PEG3350, 50MM HEPES, PH 7.0, 1.8MM SPERMINE
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Remenyi, A., (2001) Acta Crystallogr., D57, 1634.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122-24 %(v/w)PEG33501reservoir
250 mMHEPES1reservoir
31.8 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8424
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 91810 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 6.2 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OCT

1oct


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING AMINO ACID SIDE CHAINS A EXCLUDED FROM THE FINAL MODEL BECAUSE THEY HAVE POORLY DEFINED ELECTRON DENSITY: GLU 1, LYS 22, LYS 118, MET 121, LYS 125, GLU 129, LEU 133, GLU 136, LYS 142
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1007 5 %RANDOM
Rwork0.22 ---
obs0.22 19950 95.3 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 441 0 138 1631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.5
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
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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