+Open data
-Basic information
Entry | Database: PDB / ID: 1e3o | ||||||
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Title | Crystal structure of Oct-1 POU dimer bound to MORE | ||||||
Components |
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Keywords | TRANSCRIPTION / 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 / sequence-specific DNA binding / Estrogen-dependent gene expression ...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 / sequence-specific DNA binding / Estrogen-dependent gene expression / 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 / regulation of transcription by RNA polymerase II / chromatin / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Remenyi, A. / Tomilin, A. / Pohl, E. / Schoeler, H. / Wilmanns, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3o.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3o.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 1e3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3o_validation.pdf.gz | 382.1 KB | Display | wwPDB validaton report |
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Full document | 1e3o_full_validation.pdf.gz | 385.4 KB | Display | |
Data in XML | 1e3o_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 1e3o_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3o ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3o | HTTPS FTP |
-Related structure data
Related structure data | 1hf0C 1octS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: DNA chain | Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Protein | 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: NUCLEUS / Plasmid: PET-9D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14859 |
#4: Water | ChemComp-HOH / |
Compound details | CHAIN C ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % | ||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8424 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8424 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 6.2 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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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 |