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- PDB-3nd2: Structure of Yeast Importin-beta (Kap95p) -

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Basic information

Entry
Database: PDB / ID: 3nd2
TitleStructure of Yeast Importin-beta (Kap95p)
ComponentsImportin subunit beta-1
KeywordsTRANSPORT PROTEIN / importin / karyopherin / nuclear import / receptor / Nuclear Transport
Function / homology
Function and homology information


Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / regulation of nucleocytoplasmic transport / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / import into nucleus / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity ...Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / regulation of nucleocytoplasmic transport / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / import into nucleus / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into 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 / protein-containing complex binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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
Importin subunit beta-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsForwood, J.K. / Kobe, B.
CitationJournal: Structure / Year: 2010
Title: Quantitative Structural Analysis of Importin-beta Flexibility: Paradigm for Solenoid Protein Structures
Authors: Forwood, J.K. / Lange, A. / Zachariae, U. / Marfori, M. / Preast, C. / Grubmuller, H. / Stewart, M. / Corbett, A.H. / Kobe, B.
History
DepositionJun 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit beta-1


Theoretical massNumber of molelcules
Total (without water)94,8431
Polymers94,8431
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.835, 128.272, 69.050
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 94843.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q06142
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 0.1M MES pH 6.5, 20mM MgCl2, 125mM NaCl, 12% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 37902 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BKU

2bku


Resolution: 2.4→29.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 23.571 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26668 1901 5 %RANDOM
Rwork0.21254 ---
obs0.21523 35991 97.06 %-
all-37902 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20.11 Å2
2--0.41 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6653 0 0 106 6759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9629200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2815860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52625.909308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.137151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7061527
X-RAY DIFFRACTIONr_chiral_restr0.0840.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.23277
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.24806
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.54431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78326943
X-RAY DIFFRACTIONr_scbond_it1.14632638
X-RAY DIFFRACTIONr_scangle_it1.8464.52257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 143 -
Rwork0.271 2598 -
obs--94.81 %
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)
13.20072.46-1.83425.5596-0.9033.3995-0.36960.2556-0.2607-0.58690.2207-0.05940.46750.07340.14890.48910.01880.05390.10010.0183-0.185731.974-6.65234.144
21.0728-0.79920.18032.4438-2.06233.59570.1073-0.04960.02320.2327-0.03330.1019-0.40450.1012-0.0740.4812-0.03570.02010.0347-0.0266-0.126824.77224.04629.75
31.28-1.17460.14262.71960.60083.7771-0.00850.05790.03590.02530.0697-0.101-0.19580.0398-0.06120.422-0.00460.04240.00290.034-0.086422.60233.2690.638
40.4558-0.2792-0.48114.20530.24751.5344-0.07260.081-0.0257-0.18030.00720.319-0.0166-0.12460.06550.34950.0119-0.00130.1284-0.0422-0.057220.49310.118-15.146
55.54741.3332-3.93553.3516-0.97725.7977-0.0745-0.5395-0.0579-0.02040.0164-0.12380.250.430.0580.3480.0020.06970.0554-0.0341-0.097211.597-12.876-3.122
63.6308-0.4982-0.25933.51771.40493.3042-0.0525-0.27310.44950.10330.2163-0.4222-0.00570.3666-0.16380.3562-0.03840.00740.1281-0.0703-0.0377-0.621-5.14310.912
76.4433-3.15391.20946.807-0.58194.1496-0.2749-0.39530.6572-0.09570.0159-0.1721-0.6313-0.3050.2590.41990.0401-0.0150.022-0.0981-0.1402-14.4815.3828.495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 132
2X-RAY DIFFRACTION2A133 - 306
3X-RAY DIFFRACTION3A307 - 438
4X-RAY DIFFRACTION4A439 - 595
5X-RAY DIFFRACTION5A596 - 699
6X-RAY DIFFRACTION6A700 - 764
7X-RAY DIFFRACTION7A765 - 861

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