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- PDB-2k0c: Zinc-finger 2 of Nup153 -

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Basic information

Entry
Database: PDB / ID: 2k0c
TitleZinc-finger 2 of Nup153
ComponentsNuclear pore complex protein Nup153
KeywordsMETAL BINDING PROTEIN / Zinc-Finger / DNA-binding / Metal-binding / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport
Function / homology
Function and homology information


nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / negative regulation of RNA export from nucleus / annulate lamellae / Regulation of HSF1-mediated heat shock response / nuclear pore complex assembly / nuclear inclusion body / nuclear pore nuclear basket / structural constituent of nuclear pore / RNA export from nucleus / nuclear localization sequence binding / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery / small GTPase binding / protein import into nucleus / nuclear envelope / double-stranded DNA binding / nuclear membrane / chromatin binding / protein-containing complex / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / 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
Similarity search - Domain/homology
Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsBangert, J.A. / Schrader, N. / Vetter, I.R. / Stoll, R.
CitationJournal: Structure / Year: 2008
Title: The Crystal Structure of the Ran-Nup153ZnF2 Complex: a General Ran Docking Site at the Nuclear Pore Complex.
Authors: Schrader, N. / Koerner, C. / Koessmeier, K. / Bangert, J.A. / Wittinghofer, A. / Stoll, R. / Vetter, I.R.
History
DepositionJan 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6022
Polymers5,5361
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear pore complex protein Nup153 / Nucleoporin Nup153 / 153 kDa nucleoporin


Mass: 5536.296 Da / Num. of mol.: 1 / Fragment: RanBP2-type 2 domain (UNP residues 703-755)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup153 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49791
#2: Chemical ChemComp-ZN / ZINC ION


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

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.9-1.2 mM nup153znf2, 0.9-1.2 mM ZINC ION, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.9 mMnup153znf21
0.9 mMZINC ION1
Sample conditionspH: 7.0 / Pressure: ambient atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XPLOR-NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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