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Yorodumi- PDB-1cqt: CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cqt | ||||||
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Title | CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT | ||||||
Components |
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Keywords | GENE REGULATION/DNA / POU DOMAIN / PROTEIN-DNA COMPLEX / OCT1 / OCA-B / PROTEIN-DNA INTERFACE / GENE REGULATION-DNA complex | ||||||
Function / homology | Function and homology information germinal center B cell differentiation / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / humoral immune response / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / transcription coregulator activity / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / cellular response to virus ...germinal center B cell differentiation / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / humoral immune response / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / transcription coregulator activity / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / cellular response to virus / positive regulation of interleukin-6 production / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / 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 / Resolution: 3.2 Å | ||||||
Authors | Chasman, D.I. / Cepek, K. / Sharp, P.A. / Pabo, C.O. | ||||||
Citation | Journal: Genes Dev. / Year: 1999 Title: Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface. Authors: Chasman, D. / Cepek, K. / Sharp, P.A. / Pabo, C.O. #1: 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 | 1cqt.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cqt.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cqt_validation.pdf.gz | 405 KB | Display | wwPDB validaton report |
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Full document | 1cqt_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 1cqt_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1cqt_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cqt ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cqt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4657.060 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 4518.959 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 18758.367 Da / Num. of mol.: 2 / Fragment: OCT-1 POU DOMAIN, RESIDUES 278-439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: SEE REFERENCE 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14859 #4: Protein/peptide | Mass: 4874.669 Da / Num. of mol.: 2 / Fragment: OCA-B PEPTIDE, RESIDUES 1-44 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: B-CELL / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q16633 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9669 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 18, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9669 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 11803 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.45 |
Reflection shell | Resolution: 3.2→3.35 Å / Redundancy: 5.89 % / Rmerge(I) obs: 0.375 / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Num. measured all: 175486 / Biso Wilson estimate: 41.7 Å2 |
-Processing
Software |
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Refinement | Resolution: 3.2→30 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS |