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- PDB-4oih: Importin Alpha in Complex with the Bipartite NLS of Prp20 -

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Basic information

Entry
Database: PDB / ID: 4oih
TitleImportin Alpha in Complex with the Bipartite NLS of Prp20
Components
  • Guanine nucleotide exchange factor SRM1
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT/NUCLEAR PROTEIN / Bipartite NLS / Nuclear Localisation / Prp20 / PROTEIN TRANSPORT-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


response to pheromone / Postmitotic nuclear pore complex (NPC) reformation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / poly(A)+ mRNA export from nucleus / nuclear import signal receptor activity / nuclear localization sequence binding ...response to pheromone / Postmitotic nuclear pore complex (NPC) reformation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / poly(A)+ mRNA export from nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nucleus organization / ribosomal subunit export from nucleus / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / cell division / glutamatergic synapse / chromatin / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Importin subunit alpha / Atypical Arm repeat ...: / Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Guanine nucleotide exchange factor SRM1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoman, N. / Christie, M. / Swarbrick, C.M.D. / Kobe, B. / Forwood, J.K.
CitationJournal: Plos One / Year: 2013
Title: Structural Characterisation of the Nuclear Import Receptor Importin Alpha in Complex with the Bipartite NLS of Prp20
Authors: Roman, N. / Christie, M. / Swarbrick, C.M.D. / Kobe, B. / Forwood, J.K.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Guanine nucleotide exchange factor SRM1


Theoretical massNumber of molelcules
Total (without water)52,7222
Polymers52,7222
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-2 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.910, 89.920, 99.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Importin subunit alpha-2 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore ...Importin subunit alpha-2 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: UNP residues 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Guanine nucleotide exchange factor SRM1 / PrP20 / Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of ...PrP20 / Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of chromosome condensation / Suppressor of receptor mutations 1 / mRNA transport protein 1


Mass: 2835.271 Da / Num. of mol.: 1 / Fragment: UNP residues 1-25
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PRP20 / Production host: Escherichia coli (E. coli) / References: UniProt: P21827
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 500mM sodium citrate, 10mM DTT, pH 6.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K
PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2010
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954946 Å / Relative weight: 1
ReflectionResolution: 2.1→36.37 Å / Num. obs: 53834 / % possible obs: 99.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.154 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3UL1

3ul1


Resolution: 2.1→36.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.825 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20125 2126 5.1 %RANDOM
Rwork0.1677 ---
all0.1677 ---
obs0.16941 39904 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 0 125 3480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193413
X-RAY DIFFRACTIONr_bond_other_d0.0010.023391
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.9674641
X-RAY DIFFRACTIONr_angle_other_deg0.96437809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59625.597134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0821513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 170 -
Rwork0.194 2878 -
obs--100 %
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)
10.6225-0.5671-0.36860.58030.33040.3150.0287-0.09210.11560.00990.0623-0.07470.04790.0416-0.0910.0705-0.0232-0.00810.0275-0.03550.0809-1.525421.4373-0.4323
20.5088-2.0424-0.7410.1554.662.7917-0.1547-0.0408-0.12850.44470.07560.7230.20080.10510.07910.1687-0.01950.02130.1809-0.07360.3511-1.125913.8033-3.1506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 497
2X-RAY DIFFRACTION2B3 - 25

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