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- PDB-4yi0: Structure of mouse importin a1 bound to Pom121NLS -

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Basic information

Entry
Database: PDB / ID: 4yi0
TitleStructure of mouse importin a1 bound to Pom121NLS
Components
  • Importin subunit alpha-1
  • Nuclear envelope pore membrane protein POM 121
KeywordsPROTEIN TRANSPORT / karyopherin / Armadillo repeat: complex / NLS
Function / homology
Function and homology information


Postmitotic nuclear pore complex (NPC) reformation / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...Postmitotic nuclear pore complex (NPC) reformation / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / Regulation of HSF1-mediated heat shock response / nuclear pore organization / 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 / structural constituent of nuclear pore / RNA export from nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mRNA transport / nuclear pore / cytoplasmic stress granule / protein import into nucleus / host cell / nuclear membrane / DNA-binding transcription factor binding / membrane => GO:0016020 / postsynaptic density / glutamatergic synapse / endoplasmic reticulum membrane / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear pore protein POM121 / Nuclear pore complex protein / 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. ...Nuclear pore protein POM121 / Nuclear pore complex protein / 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 / 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 alpha-1 / Nuclear envelope pore membrane protein POM 121
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.806 Å
AuthorsLokareddy, R.K. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074846-01A1 United States
CitationJournal: To Be Published
Title: Mammalian Pom121 and yeast Heh2 share IBB-like NLSs that support targeting to the inner nuclear membrane
Authors: Kralt, A. / Basheer, N.J. / van den Boom, V. / Lokareddy, R.K. / Steen, A. / Cingolani, G. / Fornerod, M. / Veenhoff, L.M.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
C: Importin subunit alpha-1
A: Nuclear envelope pore membrane protein POM 121


Theoretical massNumber of molelcules
Total (without water)53,5302
Polymers53,5302
Non-polymers00
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint8 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.337, 89.753, 97.868
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 alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...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, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Nuclear envelope pore membrane protein POM 121 / Nucleoporin Nup121 / Pore membrane protein of 121 kDa / p145


Mass: 3643.055 Da / Num. of mol.: 1 / Fragment: unp residues 291-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pom121, Nup121 / Production host: Escherichia coli (E. coli) / References: UniProt: P52591
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dihydrate, 0.7 M sodium citrate tribasic dihydrate, 25 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→15.072 Å / Num. obs: 60036 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.057 / Net I/σ(I): 34.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIXdev_1696refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5U

3q5u


Resolution: 1.806→15.072 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1952 3.25 %Random selection
Rwork0.1818 ---
obs0.1827 60036 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.806→15.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 0 607 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073505
X-RAY DIFFRACTIONf_angle_d1.0944768
X-RAY DIFFRACTIONf_dihedral_angle_d14.851289
X-RAY DIFFRACTIONf_chiral_restr0.041572
X-RAY DIFFRACTIONf_plane_restr0.006613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8056-1.85070.32721150.3453462X-RAY DIFFRACTION79
1.8507-1.90070.33091370.32223812X-RAY DIFFRACTION87
1.9007-1.95650.33431280.28054025X-RAY DIFFRACTION92
1.9565-2.01950.30431310.24914146X-RAY DIFFRACTION96
2.0195-2.09150.26051590.21494247X-RAY DIFFRACTION97
2.0915-2.1750.21871310.1894260X-RAY DIFFRACTION97
2.175-2.27370.21331480.17494197X-RAY DIFFRACTION96
2.2737-2.39310.19311460.16844242X-RAY DIFFRACTION97
2.3931-2.54240.19661430.16484235X-RAY DIFFRACTION96
2.5424-2.73760.20951440.17214283X-RAY DIFFRACTION97
2.7376-3.01110.21571500.16764303X-RAY DIFFRACTION97
3.0111-3.44230.17591350.16014349X-RAY DIFFRACTION98
3.4423-4.31990.15591420.1384317X-RAY DIFFRACTION96
4.3199-15.07290.18651430.16784206X-RAY DIFFRACTION90
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)
10.85590.11890.21061.6663-0.61580.42680.063-0.0523-0.1244-0.0657-0.0266-0.08790.09720.073-0.03610.12520.0217-0.01510.11710.02640.1269-6.0311-90.5422114.0259
21.29960.9274-0.18371.6452-0.38281.39130.02490.06330.11170.0392-0.019-0.0276-0.02510.05050.00130.0751-0.0030.00480.08050.01350.12671.0482-65.7169107.49
33.62380.2119-1.63973.4816-0.16872.40020.01441.04030.2559-0.57490.08910.3752-0.0157-0.52990.27270.1602-0.0082-0.06640.38150.13010.18897.6832-51.309179.8554
43.02441.8391-2.36545.33011.01253.28740.06990.61110.1456-0.67060.62320.2482-0.0662-0.5897-0.29570.3157-0.14670.01240.19760.16750.4758-3.2548-57.043690.7338
56.3482-6.02495.78026.0174-5.37095.3858-0.8125-0.40740.52071.54140.0904-0.6603-0.74220.19010.63811.76580.16320.12582.0156-0.43241.7349-0.6717-72.421589.404
60.14040.0283-0.5690.0089-0.11532.36790.18560.3291-0.1241-1.14680.4329-1.2528-0.57650.32690.13210.3318-0.04390.17210.2542-0.04080.4432.3293-77.2514100.805
75.0856-0.0221.88956.18480.58159.84470.1982-0.2841-0.1278-0.1720.0358-0.6570.10670.2602-0.16850.10540.01040.03710.15630.03940.18692.3747-87.6109107.0979
82.67072.37140.88939.29052.49452.0282-0.2209-0.62670.02870.52070.1433-0.895-0.10210.9380.01490.6420.204-0.45351.10910.07590.7487.8015-95.2095110.7205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 73 through 222 )
2X-RAY DIFFRACTION2chain 'C' and (resid 223 through 322 )
3X-RAY DIFFRACTION3chain 'C' and (resid 323 through 497 )
4X-RAY DIFFRACTION4chain 'A' and (resid 293 through 297 )
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 307 )
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 312 )
7X-RAY DIFFRACTION7chain 'A' and (resid 313 through 317 )
8X-RAY DIFFRACTION8chain 'A' and (resid 318 through 319 )

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