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- PDB-1ko6: Crystal Structure of C-terminal Autoproteolytic Domain of Nucleop... -

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Basic information

Entry
Database: PDB / ID: 1ko6
TitleCrystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98
Components(Nuclear Pore Complex Protein Nup98) x 2
KeywordsTRANSFERASE / nucleoporin / autoproteolysis / nuclear pore
Function / homology
Function and homology information


nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein ...nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / serine-type peptidase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / nuclear periphery / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / promoter-specific chromatin binding / molecular condensate scaffold activity / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nup98, Gle2-binding sequence / 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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. ...Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nup98, Gle2-binding sequence / 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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement, MIR / Resolution: 3 Å
AuthorsHodel, A.E. / Hodel, M.R. / Griffis, E.R. / Hennig, K.A. / Ratner, G.A. / Songli, X. / Powers, M.A.
CitationJournal: Mol.Cell / Year: 2002
Title: The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98.
Authors: Hodel, A.E. / Hodel, M.R. / Griffis, E.R. / Hennig, K.A. / Ratner, G.A. / Xu, S. / Powers, M.A.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Chains A(C) and B(D) are autocatalytically cleaved between residues 863 and 864.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear Pore Complex Protein Nup98
B: Nuclear Pore Complex Protein Nup98
C: Nuclear Pore Complex Protein Nup98
D: Nuclear Pore Complex Protein Nup98


Theoretical massNumber of molelcules
Total (without water)56,6274
Polymers56,6274
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.9, 89.9, 203.2
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nuclear Pore Complex Protein Nup98 / Nucleoporin Nup98 / 98kDa nucleoporin


Mass: 21201.639 Da / Num. of mol.: 2
Fragment: C-terminal Autoproteolytic Domain (Sequence database residues 677-863)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene (production host): NUP98 / Production host: Escherichia coli (E. coli) / References: UniProt: P52948
#2: Protein Nuclear Pore Complex Protein Nup98 / Nucleoporin Nup98 / 98kDa nucleoporin


Mass: 7111.907 Da / Num. of mol.: 2
Fragment: C-terminal Autoproteolytic Domain (Sequence database residues 864-920)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene (production host): NUP98 / Production host: Escherichia coli (E. coli) / References: UniProt: P52948

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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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: MgCl, PEG8000, Tris, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 8.25
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 mMTris1drop
225 mM1dropNaCl
31 mMdithiothreitol1drop
417 %PEG80001reservoir
50.1 MTris1reservoirpH8.25
60.1 M1reservoirMgCl2
730 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 41000 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.8 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: Molecular Replacement, MIR / Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 3079 Random
Rwork0.247 --
obs-30782 -
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 0 0 2480
LS refinement shellHighest resolution: 3 Å
Refinement
*PLUS
Highest resolution: 3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.5

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