- PDB-1xke: Solution structure of the second Ran-binding domain from human RanBP2 -
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Basic information
Entry
Database: PDB / ID: 1xke
Title
Solution structure of the second Ran-binding domain from human RanBP2
Components
Ran-binding protein 2
Keywords
PROTEIN TRANSPORT / beta barrel / pleckstrin-homology (PH) domain / phosphotyrosine-binding (PTB) domain
Function / homology
Function and homology information
cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / GTPase activator activity / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / small GTPase binding / HCMV Early Events / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / protein folding / nuclear envelope / snRNP Assembly / nuclear membrane / intracellular membrane-bounded organelle / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Roll / Mainly Beta Similarity search - Domain/homology
Ionic strength: 150 mM Na2SO4 / pH: 6.5 / Pressure: ambient / Temperature: 298 K
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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
800
2
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
2.6
Bruker
collection
XwinNMR
2.6
Bruker
processing
AUREMOL
2.0.3
Gronwald,W. andKalbitzer,H.R.
dataanalysis
CNS
1.1
structuresolution
CNS
1.1
refinement
XPLOR-NIH
2.9.6
structuresolution
Refinement
Method: simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 1492 restraints (1281 NOE-derived distance restraints, 182 dihedral angle restraints and 29 hydrogen bond restraints). The structures were also refined ...Details: The structures are based on a total of 1492 restraints (1281 NOE-derived distance restraints, 182 dihedral angle restraints and 29 hydrogen bond restraints). The structures were also refined in water using XPLOR-NIH 2.9.6 using the protocol of Linge et al. (Linge, J. P., Williams, M. A., Spronk, C. A., Bonvin, A. M., & Nilges, M. ,2003. Refinement of protein structures in explicit solvent. Proteins 50, 496-506).
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20
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