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- PDB-4b18: The crystal structure of human Importin alpha 5 with TERT NLS peptide -

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Basic information

Entry
Database: PDB / ID: 4b18
TitleThe crystal structure of human Importin alpha 5 with TERT NLS peptide
Components
  • IMPORTIN SUBUNIT ALPHA-1
  • TELOMERASE REVERSE TRANSCRIPTASE
KeywordsTRANSPORT PROTEIN / PEPTIDE / TRANSPORT PROTEIN - PEPTIDE COMPLEX
Function / homology
Function and homology information


satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / Inhibition of nitric oxide production / positive regulation of protein localization to nucleolus ...satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / Inhibition of nitric oxide production / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / regulation of DNA recombination / establishment of protein localization to telomere / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Transport of Ribonucleoproteins into the Host Nucleus / nuclear telomere cap complex / siRNA processing / NS1 Mediated Effects on Host Pathways / telomere maintenance via recombination / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / nuclear localization sequence binding / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / regulation of canonical Wnt signaling pathway / nuclear import signal receptor activity / RNA-templated transcription / DNA biosynthetic process / telomeric DNA binding / positive regulation of stem cell proliferation / Vpr-mediated nuclear import of PICs / Integration of provirus / mitochondrial nucleoid / negative regulation of cellular senescence / Telomere Extension By Telomerase / replicative senescence / positive regulation of Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / telomere maintenance via telomerase / nuclear pore / RNA-directed DNA polymerase activity / negative regulation of endothelial cell apoptotic process / response to cadmium ion / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of nitric-oxide synthase activity / Assembly of the ORC complex at the origin of replication / positive regulation of D-glucose import / mitochondrion organization / Formation of the beta-catenin:TCF transactivating complex / transcription coactivator binding / regulation of protein stability / PML body / positive regulation of miRNA transcription / ISG15 antiviral mechanism / RNA-directed DNA polymerase / telomerase activity / protein import into nucleus / positive regulation of angiogenesis / Interferon alpha/beta signaling / positive regulation of protein binding / protein-folding chaperone binding / heart development / regulation of apoptotic process / cellular response to hypoxia / negative regulation of neuron apoptotic process / tRNA binding / chromosome, telomeric region / postsynaptic density / nuclear speck / negative regulation of gene expression / RNA-directed RNA polymerase activity / dendrite / nucleolus / glutamatergic synapse / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / DNA/RNA polymerase superfamily / Mainly Alpha
Similarity search - Domain/homology
Telomerase reverse transcriptase / Importin subunit alpha-5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsKim, K.L. / Yoo, J.H. / Cho, H.S.
CitationJournal: J.Cell.Sci. / Year: 2015
Title: Akt-Mediated Phosphorylation Increases the Binding Affinity of Htert for Importin Alpha to Promote Nuclear Translocation.
Authors: Jeong, S.A. / Kim, K. / Lee, J.H. / Cha, J.S. / Khadka, P. / Cho, H. / Chung, I.K.
History
DepositionJul 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Derived calculations / Source and taxonomy
Revision 1.3Jun 24, 2015Group: Database references
Revision 1.4Jul 1, 2015Group: Database references
Revision 1.5Dec 20, 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 SUBUNIT ALPHA-1
B: TELOMERASE REVERSE TRANSCRIPTASE


Theoretical massNumber of molelcules
Total (without water)51,6842
Polymers51,6842
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.723, 59.916, 69.331
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1 / KARYOPHERIN SUBUNIT ALPHA-1 / NUCLEOPROTEIN INTERACTOR 1 / NPI-1 / RAG COHORT PROTEIN 2 / SRP1-BETA


Mass: 49401.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 66-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): CODON PLUS / References: UniProt: P52294
#2: Protein/peptide TELOMERASE REVERSE TRANSCRIPTASE / HEST2 / TELOMERASE CATALYTIC SUBUNIT / TELOMERASE-ASSOCIATED PROTEIN 2 / TP2


Mass: 2282.704 Da / Num. of mol.: 1 / Fragment: TERT NLS PEPTIDE, RESIDUES 222-240 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O14746, RNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.19 Å3/Da / Density % sol: 61.44 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 21441 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 2.56→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JDQ

2jdq


Resolution: 2.52→70 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.026 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1101 5.1 %RANDOM
Rwork0.19818 ---
obs0.20101 20339 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-1.13 Å2
2--3.61 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.52→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 0 14 3464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9714762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46824.702151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.75515624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5581523
X-RAY DIFFRACTIONr_chiral_restr0.1280.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212598
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 76 -
Rwork0.259 1272 -
obs--86.02 %

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