- PDB-2fk4: Solution structure of the C-terminal zinc binding domain of the H... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2fk4
Title
Solution structure of the C-terminal zinc binding domain of the HPV16 E6 oncoprotein
Components
Protein E6
Keywords
Metal binding protein / Oncoprotein / ZINC BINDING DOMAIN
Function / homology
Function and homology information
symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion binding Similarity search - Function
E6 early regulatory protein / CRO Repressor / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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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
2
2
2
2D NOESY
NMR details
Text: This structure was determined using standard 2D homonuclear and 3D 15N heteronuclear techniques.
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.0 mM E6C U-15N; 20 mM TRIS-HCl, 50 mM NaCl, 1mM DTT
90% H2O/10% D2O
2
1.0 mM E6C, 20 mM TRIS-HCl, 50 mM NaCl, 1mM DTT
90% H2O/10% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
50mM
6.8
ambient
288K
2
50mM
6.8
ambient
288K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DRX
Bruker
DRX
600
1
Bruker DRX
Bruker
DRX
500
2
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Processing
NMR software
Name
Version
Developer
Classification
X-PLOR
NIH
Brunger
structuresolution
XEASY
1
Bartels
dataanalysis
XwinNMR
2.6
Bruker
processing
X-PLOR
NIH
Brunger
refinement
Refinement
Method: simulated annealing, protocol refine.inp / Software ordinal: 1 Details: NOE distance restraints were split in two sets. One set involved residues that were identified as beeing affected by conformational exchange by relaxation dispersion experiments. These ...Details: NOE distance restraints were split in two sets. One set involved residues that were identified as beeing affected by conformational exchange by relaxation dispersion experiments. These distances were assigned an additional 1A to the upper distance limit. Reported close contacts are due to conformational heterogeneities in the set of NOES. The dynamical properties of this protein have been described in depth in the J. Biomol. NMR reference cited above.
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 10
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