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Yorodumi- PDB-1vol: TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vol | ||||||
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Title | TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION INITIATION / MOLECULAR RECOGNITION / COMPLEX / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION / DNA / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II complex binding / protein acetylation / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / viral transcription / acetyltransferase activity / RNA polymerase II transcribes snRNA genes / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / promoter-specific chromatin binding / protein-DNA complex / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / kinetochore / RNA polymerase II transcription regulator complex / chromosome / DNA-binding transcription factor binding / transcription by RNA polymerase II / nuclear body / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Nikolov, D.B. / Chen, H. / Halay, E.D. / Usheva, A.U. / Hisatake, K. / Lee, D.K. / Roeder, R.G. / Burley, S.K. | ||||||
Citation | Journal: Nature / Year: 1995 Title: Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Authors: Nikolov, D.B. / Chen, H. / Halay, E.D. / Usheva, A.A. / Hisatake, K. / Lee, D.K. / Roeder, R.G. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vol.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vol.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/1vol ftp://data.pdbj.org/pub/pdb/validation_reports/vo/1vol | 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: 4987.253 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4809.129 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 22767.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403 |
#4: Protein | Mass: 22400.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P28147 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.7 Å / Num. obs: 20995 / % possible obs: 82.1 % / Rsym value: 0.072 |
Reflection | *PLUS Highest resolution: 2.7 Å / % possible obs: 82.1 % / Num. measured all: 180515 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Resolution: 2.7→8 Å
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |