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Yorodumi- PDB-1oct: CRYSTAL STRUCTURE OF THE OCT-1 POU DOMAIN BOUND TO AN OCTAMER SIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oct | ||||||
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Title | CRYSTAL STRUCTURE OF THE OCT-1 POU DOMAIN BOUND TO AN OCTAMER SITE: DNA RECOGNITION WITH TETHERED DNA-BINDING MODULES | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Klemm, J.D. / Rould, M.A. / Aurora, R. / Herr, W. / Pabo, C.O. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1994 Title: Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Authors: Klemm, J.D. / Rould, M.A. / Aurora, R. / Herr, W. / Pabo, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oct.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oct.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1oct ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1oct | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4657.060 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4518.959 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 18014.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14859 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.34 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 6998 / % possible obs: 96 % / Num. measured all: 22955 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Resolution: 3→20 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. reflection all: 6998 / σ(F): 0 / Rfactor obs: 0.237 / Rfactor Rwork: 0.237 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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