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- PDB-2c1m: Nup50:importin-alpha complex -

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Basic information

Entry
Database: PDB / ID: 2c1m
TitleNup50:importin-alpha complex
Components
  • IMPORTIN-ALPHA2 SUBUNIT
  • NUCLEOPORIN 50 KDA
KeywordsPROTEIN TRANSPORT/MEMBRANE PROTEIN / NUCLEAR TRANSPORT-COMPLEX / IMPORTIN-ALPHA / NUCLEOPORIN NUP50 / NUCLEAR TRANSPORT-COMPLEX NUP50 / NUCLEAR PROTEIN / PROTEIN TRANSPORT / PROTEIN TRANSPORT-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / neural tube formation / 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 / host cell / 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 / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / ribonucleoprotein complex / intracellular membrane-bounded organelle / glutamatergic synapse / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / 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 / PH-like domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Nuclear pore complex protein Nup50
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMatsuura, Y. / Stewart, M.
CitationJournal: Embo J. / Year: 2005
Title: Nup50/Npap60 Function in Nuclear Protein Import Complex Disassembly and Importin Recycling.
Authors: Matsuura, Y. / Stewart, M.
History
DepositionSep 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN-ALPHA2 SUBUNIT
B: NUCLEOPORIN 50 KDA


Theoretical massNumber of molelcules
Total (without water)51,4252
Polymers51,4252
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.467, 74.467, 188.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein IMPORTIN-ALPHA2 SUBUNIT / KARYOPHERIN ALPHA-2 SUBUNIT / SRP1-ALPHA / PENDULIN / RAG COHORT PROTEIN 1 / PORE TARGETING COMPLEX ...KARYOPHERIN ALPHA-2 SUBUNIT / SRP1-ALPHA / PENDULIN / RAG COHORT PROTEIN 1 / PORE TARGETING COMPLEX 58 KDA SUBUNIT / PTAC58 / IMPORTIN ALPHA P1


Mass: 45985.676 Da / Num. of mol.: 1 / Fragment: DELTA IBB, RESIDUES 75-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52293
#2: Protein/peptide NUCLEOPORIN 50 KDA / NUP50 / NUCLEAR PORE-ASSOCIATED PROTEIN 60 KDA-LIKE


Mass: 5439.141 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9JIH2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIMPORTIN-ALPHA2 SUBUNIT: INVOLVED IN NUCLEAR PROTEIN IMPORT AS AN ADAPTER PROTEIN FOR NUCLEAR ...IMPORTIN-ALPHA2 SUBUNIT: INVOLVED IN NUCLEAR PROTEIN IMPORT AS AN ADAPTER PROTEIN FOR NUCLEAR RECEPTOR KPNB1. NUCLEOPORIN 50 KDA: INVOLVED IN NUCLEAR PROTEIN EXPORT.

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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: 2.53 Å3/Da / Density % sol: 51.47 % / Description: COMPLETE DETAILS GIVEN IN PUBLICATION
Crystal growDetails: DETAILS GIVEN IN PUBLICATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
DetectorDate: Mar 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 27445 / % possible obs: 98.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNS9refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAL

1ial


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML / Details: FOR DETAILS SEE PUBLICATION
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1377 5 %RANDOM
Rwork0.2214 ---
obs0.2214 27377 98.7 %-
Solvent computationBsol: 32.2152 Å2 / ksol: 0.332386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.182 Å20 Å20 Å2
2--0.182 Å20 Å2
3----0.363 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 0 116 3728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006336
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.14954
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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