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- PDB-1xke: Solution structure of the second Ran-binding domain from human RanBP2 -

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Basic information

Entry
Database: PDB / ID: 1xke
TitleSolution structure of the second Ran-binding domain from human RanBP2
ComponentsRan-binding protein 2
KeywordsPROTEIN 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 activity / SUMO ligase complex / 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 activity / SUMO ligase complex / 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 / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / 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 / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / protein sumoylation / Signaling by ALK fusions and activated point mutants / 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 / 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 / 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 / cytosol / cytoplasm
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
E3 SUMO-protein ligase RanBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGeyer, J.P. / Doeker, R. / Kremer, W. / Zhao, X. / Kuhlmann, J. / Kalbitzer, H.R.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Solution structure of the Ran-binding domain 2 of RanBP2 and its interaction with the C terminus of Ran.
Authors: Geyer, J.P. / Doker, R. / Kremer, W. / Zhao, X. / Kuhlmann, J. / Kalbitzer, H.R.
#1: Journal: J.Biomol.Nmr / Year: 2002
Title: Sequence-specific resonance assignment of the second Ran-binding domain of human RanBP2
Authors: Doeker, R. / Zhao, X. / Kremer, W. / Villa, B. / Kuhlmann, J. / Kalbitzer, H.R.
History
DepositionSep 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ran-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,1381
Polymers15,1381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ran-binding protein 2 / RanBP2 / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / 358 kDa nucleoporin / P270


Mass: 15138.471 Da / Num. of mol.: 1 / Fragment: Ran-binding domain 2 (RanBD2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49792

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1242D NOESY
1313D 15N-separated NOESY
1423D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM RanBD2 U-13C; U-15N; 150mM Na2SO4; 10mM DTE; 0.5 mM EDTA; 1mM NaN3; 0.1mM DSS; 10mM potassium phosphate buffer at pH 6.5;92% H2O, 8%D2O
20.7mM RanBD2 U-13C; U-15N; 150mM Na2SO4; 10mM DTE; 0.5mM EDTA; 1mM NaN3; 0.1mM DSS; 10mM potassium phosphate buffer at pH 6.5;100% D2O
31.0mM RanBD2 U-15N; 150mM Na2SO4; 10mM DTE; 0.5mM EDTA; 1mM NaN3; 0.1 mM DSS; 10mM potassium phosphate buffer at pH 6.5;92% H2O, 8%D2O
41.0mM RanBD2 U-15N; 150mM Na2SO4; 10mM DTE; 0.5mM EDTA; 1mM NaN3; 0.1mM DSS; 10mM potassium phosphate buffer at pH 6.5;100% D2O
Sample conditionsIonic strength: 150 mM Na2SO4 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
AUREMOL2.0.3Gronwald,W. and Kalbitzer,H.R.data analysis
CNS1.1structure solution
CNS1.1refinement
XPLOR-NIH2.9.6structure solution
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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