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- PDB-1pjm: Mouse Importin alpha-bipartite NLS from human retinoblastoma prot... -

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Basic information

Entry
Database: PDB / ID: 1pjm
TitleMouse Importin alpha-bipartite NLS from human retinoblastoma protein Complex
Components
  • Importin alpha-2 subunitImportin α
  • Retinoblastoma-associated protein
KeywordsPROTEIN TRANSPORT / IMPORTIN ALPHA/KARYOPHERIN ALPHA / NUCLEAR LOCALIZATION SEQUENCE (NLS) RECOGNITION / BIPARTITE NLS / HUMAN RETINOBLASTOMA PROTEIN
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / Sensing of DNA Double Strand Breaks / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of centromere complex assembly / positive regulation of macrophage differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / tissue homeostasis / glial cell apoptotic process / positive regulation of viral life cycle / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / positive regulation of transcription regulatory region DNA binding / neuron maturation / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / digestive tract development / aortic valve morphogenesis / myoblast differentiation / Replication of the SARS-CoV-1 genome / SWI/SNF complex / negative regulation of cold-induced thermogenesis / nuclear import signal receptor activity / nuclear localization sequence binding / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / NLS-bearing protein import into nucleus / negative regulation of G1/S transition of mitotic cell cycle / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / hepatocyte apoptotic process / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / glial cell proliferation / Nuclear events stimulated by ALK signaling in cancer / chondrocyte differentiation / heterochromatin formation / negative regulation of smoothened signaling pathway / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / host cell / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of protein kinase activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / negative regulation of cell growth / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / negative regulation of inflammatory response / cytoplasmic stress granule / spindle / protein import into nucleus / cellular response to insulin stimulus / transcription corepressor activity / Cyclin D associated events in G1 / neuron projection development / negative regulation of epithelial cell proliferation / disordered domain specific binding / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / spermatogenesis / neuron apoptotic process / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / transcription by RNA polymerase II / postsynaptic density / molecular adaptor activity / cell differentiation / regulation of cell cycle / chromatin remodeling / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / glutamatergic synapse
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal 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 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-associated protein / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsFontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Kobe, B.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Biophysical Characterization of Interactions Involving Impostin-alpha during Nuclear Import
Authors: Catimel, B. / Teh, T. / Fontes, M.R.M. / Jennings, I.G. / Jans, D. / Howlett, G.J. / Nice, E.C. / Kobe, B.
#3: Journal: Nat.Struct.Biol. / Year: 1999
Title: Autoinhibition by an internal nuclear localization signal reveled by the crystal structure of mammalian importin alpha
Authors: Kobe, B.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoblastoma-associated protein
B: Importin alpha-2 subunit


Theoretical massNumber of molelcules
Total (without water)52,0162
Polymers52,0162
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-1 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 89.179, 100.992
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/peptide Retinoblastoma-associated protein


Mass: 2129.530 Da / Num. of mol.: 1
Fragment: NLS (nuclear localization signal) bipartite peptide
Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN HUMAN RETINOBLASTOMA PROTEIN
References: UniProt: P06400
#2: Protein Importin alpha-2 subunit / Importin α / Karyopherin alpha-2 subunit


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: NLS binding domain (70-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: KPNA2 OR RCH1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 mg/mlprotein1drop
20.6 Msodium citrate1reservoirpH6.0
310 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 25382 / Num. obs: 25382 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 249870
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY: 1ial

1ial


Resolution: 2.5→29.57 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1169 4.8 %RANDOM
Rwork0.204 ---
obs0.204 24323 96 %-
all-24323 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.52 Å2 / ksol: 0.363607 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---6.09 Å20 Å2
3---6.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 173 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.552.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 198 4.9 %
Rwork0.264 3877 -
obs-4075 98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.263

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