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Yorodumi- PDB-1k99: Solution Structure of the first HMG box in human Upstream binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k99 | ||||||
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Title | Solution Structure of the first HMG box in human Upstream binding factor | ||||||
Components | Upstream binding factor 1Transcription factor | ||||||
Keywords | DNA BINDING PROTEIN / alpha-helix / L-shape | ||||||
Function / homology | Function and homology information RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA Polymerase I Transcription Termination / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape ...RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA Polymerase I Transcription Termination / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / fibrillar center / scaffold protein binding / chromatin binding / nucleolus / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing; torsion angle dynamics | ||||||
Authors | Xu, Y. / Yang, W. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Solution structure of the first HMG box domain in human upstream binding factor. Authors: Xu, Y. / Yang, W. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k99.cif.gz | 630 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k99.ent.gz | 531.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k99 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k99 | 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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NMR ensembles |
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-Components
#1: Protein | Mass: 12399.603 Da / Num. of mol.: 1 / Fragment: HMG box 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hUBF(103-192) / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17480 |
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-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 |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing; torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 60 / Conformers submitted total number: 20 |