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- PDB-2aiv: Multiple conformations in the ligand-binding site of the yeast nu... -

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Basic information

Entry
Database: PDB / ID: 2aiv
TitleMultiple conformations in the ligand-binding site of the yeast nuclear pore targeting domain of NUP116P
Componentsfragment of Nucleoporin NUP116/NSP116
KeywordsTRANSPORT PROTEIN / Beta sandwich
Function / homology
Function and homology information


nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport ...nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / nuclear localization sequence binding / ribosomal large subunit export from nucleus / mRNA export from nucleus / nuclear pore / protein import into nucleus / nuclear envelope / ATPase binding / nuclear membrane / RNA binding / identical protein binding
Similarity search - Function
Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoporin NUP116/NSP116
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsRobinson, M.A. / Park, S. / Sun, Z.-Y.J. / Silver, P. / Wagner, G. / Hogle, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Multiple Conformations in the Ligand-binding Site of the Yeast Nuclear Pore-targeting Domain of Nup116p
Authors: Robinson, M.A. / Park, S. / Sun, Z.-Y.J. / Silver, P.A. / Wagner, G. / Hogle, J.M.
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fragment of Nucleoporin NUP116/NSP116


Theoretical massNumber of molelcules
Total (without water)16,8081
Polymers16,8081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein fragment of Nucleoporin NUP116/NSP116 / Nup116p / Nuclear pore protein NUP116/NSP116


Mass: 16808.256 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 967-1113
Source method: isolated from a genetically manipulated source
Details: fragment Interacting with NUP82 NPC subcomplex
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP116, NSP116 / Plasmid: pDEST 15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q02630

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
151

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Sample preparation

DetailsContents: 0.5-1mM Nup116p U-15N,13C
Solvent system: 100mM sodium-potassium phosphate pH 6.5, 50mM NaCl, 1mM DTT, 90% H2O, 10% D2O
Sample conditionsIonic strength: 100mM sodium-potassium phosphate pH 6.5, 50mM NaCl, 1mM DTT
pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Varian UNITYPLUSVarianUNITYPLUS7503
Varian INOVAVarianINOVA5004
Varian UNITYPLUSVarianUNITYPLUS4005
Varian INOVAVarianINOVA6006

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.structure solution
DYANA1Guentert, P.structure solution
NMRPipeJuly 2004 versionDelaglio, F.processing
DYANA1Guentert, P.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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