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- PDB-3tkn: Structure of the Nup82-Nup159-Nup98 heterotrimer -

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Basic information

Entry
Database: PDB / ID: 3tkn
TitleStructure of the Nup82-Nup159-Nup98 heterotrimer
Components
  • Nucleoporin 98
  • Nucleoporin NUP159
  • Nucleoporin NUP82
KeywordsPROTEIN TRANSPORT / protein complex / oncoprotein
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore linkers / : / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / nuclear pore localization / adenyl-nucleotide exchange factor activity / nuclear pore central transport channel / RHO GTPases Activate Formins / Separation of Sister Chromatids / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear inclusion body / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / mRNA transport / ribosomal small subunit export from nucleus / mRNA export from nucleus / nuclear pore / protein export from nucleus / serine-type peptidase activity / nuclear periphery / promoter-specific chromatin binding / peptide binding / protein import into nucleus / transcription corepressor activity / nuclear envelope / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase ...Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / 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 / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoporin NUP82 / Nucleoporin NUP159 / Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsStuwe, T.T. / Hoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Molecular basis for the anchoring of proto-oncoprotein nup98 to the cytoplasmic face of the nuclear pore complex.
Authors: Stuwe, T. / Schada von Borzyskowski, L. / Davenport, A.M. / Hoelz, A.
History
DepositionAug 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Feb 28, 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: Nucleoporin NUP82
B: Nucleoporin NUP159
C: Nucleoporin 98
D: Nucleoporin NUP82
E: Nucleoporin NUP159
F: Nucleoporin 98
G: Nucleoporin NUP82
H: Nucleoporin NUP159
I: Nucleoporin 98


Theoretical massNumber of molelcules
Total (without water)219,1289
Polymers219,1289
Non-polymers00
Water00
1
A: Nucleoporin NUP82
B: Nucleoporin NUP159
C: Nucleoporin 98


Theoretical massNumber of molelcules
Total (without water)73,0433
Polymers73,0433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-20 kcal/mol
Surface area29130 Å2
MethodPISA
2
D: Nucleoporin NUP82
E: Nucleoporin NUP159
F: Nucleoporin 98


Theoretical massNumber of molelcules
Total (without water)73,0433
Polymers73,0433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-20 kcal/mol
Surface area28470 Å2
MethodPISA
3
G: Nucleoporin NUP82
H: Nucleoporin NUP159
I: Nucleoporin 98


Theoretical massNumber of molelcules
Total (without water)73,0433
Polymers73,0433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.905, 115.849, 118.488
Angle α, β, γ (deg.)90.000, 111.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoporin NUP82 / Nuclear pore protein NUP82


Mass: 51607.301 Da / Num. of mol.: 3 / Fragment: UNP residues 1-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRB187, J1135, NUP82, YJL061W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P40368
#2: Protein/peptide Nucleoporin NUP159 / Nuclear pore protein NUP159


Mass: 4319.120 Da / Num. of mol.: 3 / Fragment: UNP residues 1425-1460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP158, NUP159, RAT7, YIL115C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P40477
#3: Protein Nucleoporin 98


Mass: 17116.346 Da / Num. of mol.: 3 / Fragment: UNP residues 732-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nup98 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q6PFD9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 37089 / Num. obs: 34404 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.018 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 3437 9.3 %RANDOM
Rwork0.2492 ---
all-37089 --
obs-34404 --
Solvent computationBsol: 33.0094 Å2
Displacement parametersBiso max: 199.47 Å2 / Biso mean: 113.9914 Å2 / Biso min: 58.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.314 Å20 Å21.099 Å2
2---5.626 Å20 Å2
3---8.94 Å2
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15021 0 0 0 15021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_scbond_it1.1642
X-RAY DIFFRACTIONc_mcangle_it2.3132
X-RAY DIFFRACTIONc_scangle_it1.9992.5
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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