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- PDB-5owu: Kap95:Nup1 complex -

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Basic information

Entry
Database: PDB / ID: 5owu
TitleKap95:Nup1 complex
Components
  • Importin subunit beta-1
  • Nucleoporin NUP1
KeywordsTRANSPORT PROTEIN / nuclear transport
Function / homology
Function and homology information


Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response ...Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / protein targeting to membrane / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / small GTPase binding / protein import into nucleus / disordered domain specific binding / nuclear envelope / nuclear membrane / protein-containing complex binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear pore complex protein / Importin beta family / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 ...Nuclear pore complex protein / Importin beta family / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP1 / Importin subunit beta-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStewart, M.
CitationJournal: J. Mol. Biol. / Year: 2005
Title: Structural basis for the high-affinity binding of nucleoporin Nup1p to the Saccharomyces cerevisiae importin-beta homologue, Kap95p.
Authors: Liu, S.M. / Stewart, M.
History
DepositionSep 4, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionOct 25, 2017ID: 2BPT
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit beta-1
B: Nucleoporin NUP1


Theoretical massNumber of molelcules
Total (without water)208,5572
Polymers208,5572
Non-polymers00
Water12,502694
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SDS-PAGE showed equimolar quantities of both proteins after gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-19 kcal/mol
Surface area39660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.372, 126.534, 69.649
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Importin subunit beta-1 / Importin-95 / Karyopherin subunit beta-1 / Karyopherin-95


Mass: 94843.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: KAP95, YLR347C, L8300.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06142
#2: Protein Nucleoporin NUP1 / Nuclear pore protein NUP1


Mass: 113713.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP1, YOR098C, YOR3182C / Production host: Escherichia coli (E. coli) / References: UniProt: P20676
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 5 mg/ml protein in 5 mM Tris-HCl, pH 7.4 equilibrated against 90 mM (NH4)2SO4, 50 mM Na Cacodylate, pH 6.5, 13% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→28.723 Å / Num. all: 600763 / Num. obs: 66945 / % possible obs: 99.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.2
Reflection shellRedundancy: 8.4 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.5 / Num. unique all: 81491 / Num. unique obs: 9691 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.723 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2193 3354 5.07 %
Rwork0.1733 --
obs0.1756 66164 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6860 0 0 694 7554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057081
X-RAY DIFFRACTIONf_angle_d0.6439651
X-RAY DIFFRACTIONf_dihedral_angle_d11.6224353
X-RAY DIFFRACTIONf_chiral_restr0.0391124
X-RAY DIFFRACTIONf_plane_restr0.0041266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02860.31461550.26142603X-RAY DIFFRACTION99
2.0286-2.05890.25681440.23952632X-RAY DIFFRACTION100
2.0589-2.0910.25941390.21592650X-RAY DIFFRACTION100
2.091-2.12530.28911370.21172651X-RAY DIFFRACTION100
2.1253-2.16190.22011430.20312640X-RAY DIFFRACTION100
2.1619-2.20120.24741260.19512615X-RAY DIFFRACTION100
2.2012-2.24350.26291490.19082681X-RAY DIFFRACTION100
2.2435-2.28930.25881500.18312620X-RAY DIFFRACTION100
2.2893-2.33910.22741210.17972671X-RAY DIFFRACTION100
2.3391-2.39350.2451430.17472640X-RAY DIFFRACTION100
2.3935-2.45330.21841300.17122619X-RAY DIFFRACTION100
2.4533-2.51960.2091440.17412659X-RAY DIFFRACTION100
2.5196-2.59370.26521410.1682626X-RAY DIFFRACTION100
2.5937-2.67730.22821500.172663X-RAY DIFFRACTION100
2.6773-2.7730.22241600.17572631X-RAY DIFFRACTION100
2.773-2.88390.19031240.16812648X-RAY DIFFRACTION100
2.8839-3.0150.21161320.17752655X-RAY DIFFRACTION100
3.015-3.17380.25441340.17922645X-RAY DIFFRACTION100
3.1738-3.37230.19891460.17682613X-RAY DIFFRACTION99
3.3723-3.63220.23931630.17272604X-RAY DIFFRACTION98
3.6322-3.99690.19411440.15862572X-RAY DIFFRACTION97
3.9969-4.57320.17161280.14572526X-RAY DIFFRACTION94
4.5732-5.75420.19071320.15482600X-RAY DIFFRACTION97
5.7542-28.7260.21881190.17782346X-RAY DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79410.1566-0.44251.0453-0.36520.9968-0.15160.0429-0.03610.0150.0095-0.01920.12020.0527-00.163-0.0136-0.01650.22260.01760.193162.5907-41.595235.4756
20.4422-0.07020.12420.4345-0.9481.2051-0.01590.0403-0.06140.1598-0.03950.0848-0.23770.0594-0.00020.36070.0078-0.03940.2505-0.01240.244454.5994-12.735119.4464
30.1979-0.0608-0.02720.81770.04570.2476-0.0303-0.0161-0.0453-0.04020.0139-0.031-0.0254-0.034700.17450.00290.01450.2050.00410.202648.1707-26.7087-14.1744
40.71310.0355-0.85141.12440.03721.15890.05330.00110.05810.0561-0.0622-0.0444-0.1993-0.0132-00.2338-0.0437-0.03760.26350.01370.258827.1406-46.20566.7847
50.0115-0.0025-0.00410.0898-0.0008-0.01090.4606-0.23490.05720.5549-0.2160.21730.0235-0.2719-00.5133-0.0164-0.02850.30870.01580.300651.2521.527422.9854
60.0963-0.02040.00820.1037-0.03980.01770.25640.02620.4334-0.1517-0.0724-0.2792-0.0723-0.0115-0.00151.1366-0.08250.02010.4477-0.06860.433362.4975-7.205140.4658
70.00660.0018-0.00270.00010.00280.0018-0.01520.11450.07330.07430.14960.1625-0.0596-0.0026-00.66230.0658-0.00790.43240.00850.40352.8302-11.215942.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 173 )
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 346 )
3X-RAY DIFFRACTION3chain 'A' and (resid 347 through 614 )
4X-RAY DIFFRACTION4chain 'A' and (resid 615 through 861 )
5X-RAY DIFFRACTION5chain 'B' and (resid 974 through 988 )
6X-RAY DIFFRACTION6chain 'B' and (resid 999 through 1006 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1007 through 1012 )

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