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Yorodumi- PDB-1rly: RDC-derived models of the zinc ribbon domain of human general tra... -
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-Basic information
Entry | Database: PDB / ID: 1rly | ||||||
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Title | RDC-derived models of the zinc ribbon domain of human general transcription TFIIB (zinc bound structures) | ||||||
Components | Transcription initiation factor IIB | ||||||
Keywords | METAL BINDING PROTEIN / Zinc ribbon / Rubredoxin knuckle | ||||||
Function / homology | Function and homology information positive regulation of core promoter binding / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / germinal vesicle / transcription preinitiation complex / nuclear thyroid hormone receptor binding / protein acetylation / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / germinal vesicle / transcription preinitiation complex / nuclear thyroid hormone receptor 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 / cell division site / RNA polymerase II complex binding / viral transcription / acetyltransferase activity / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / 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 / 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 / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Ghosh, M. / Ikura, M. | ||||||
Citation | Journal: Biochem.J. / Year: 2004 Title: Probing Zn2+-binding effects on the zinc-ribbon domain of human general transcription factor TFIIB. Authors: Ghosh, M. / Elsby, L.M. / Mal, T.K. / Gooding, J.M. / Roberts, S.G. / Ikura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rly.cif.gz | 430.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rly.ent.gz | 367.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rly_validation.pdf.gz | 349.2 KB | Display | wwPDB validaton report |
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Full document | 1rly_full_validation.pdf.gz | 543.8 KB | Display | |
Data in XML | 1rly_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 1rly_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/1rly ftp://data.pdbj.org/pub/pdb/validation_reports/rl/1rly | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6571.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TFIIB, TF2B / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00403 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: the structures are based on a total of 476 restraints, 443 are distance constraints, 10 zinc coordination restraints,23 1H-15N RDC restraints | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 25 / Conformers submitted total number: 25 |