- PDB-1l8y: Solution structure of HMG box 5 in human upstream binding factor -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1l8y
Title
Solution structure of HMG box 5 in human upstream binding factor
Components
upstream binding factor 1
Keywords
DNA BINDING PROTEIN / hUBF / HMG box 5 / DNA binding domain
Function / homology
Function and homology information
RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Transcription Termination / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape ...RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Transcription Termination / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / 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
High mobility group box domain 5 / : / HMG (high mobility group) box 5 / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...High mobility group box domain 5 / : / HMG (high mobility group) box 5 / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 10891.573 Da / Num. of mol.: 1 / Fragment: HMG box 5 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17480
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 15N-separated NOESY
1
2
1
3D 13C-separated NOESY
1
3
2
3D 13C-separated NOESY
NMR details
Text: The structure was determined using triple-resonance NMR spectroscopy
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
3mM hUBF HMG box 5, U-15N, 13C; 45mM NaPO4
90% H2O/10% D2O
2
3mM hUBF HMG box 5, U-15N, 13C; 45mM NaPO4
100% D2O
Sample conditions
Ionic strength: 45 mM NaPO4 / pH: 5.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz
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Processing
NMR software
Name
Version
Developer
Classification
NMRPipp
F.DelagioandA.Bax
processing
PIPP
D.S.Garrett
dataanalysis
CNS
1
A.T.Brunger
structuresolution
CNS
A.T.Brunger
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: The structures are based on the total number constraints of 1220, including 1098 NOE-derived distance constraints, 104 dihedral angle constraints, 18 hydrogen bond constraints.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 30
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