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- PDB-5umz: Structure of TNRC6A NLS in complex with importin-alpha -

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Basic information

Entry
Database: PDB / ID: 5umz
TitleStructure of TNRC6A NLS in complex with importin-alpha
Components
  • Importin subunit alpha-1
  • TNRC6A
KeywordsPROTEIN TRANSPORT / mRNA decay / miRNA ARM repeat / nuclear transport
Function / homology
Function and homology information


Post-transcriptional silencing by small RNAs / Transcriptional regulation by small RNAs / Sensing of DNA Double Strand Breaks / maintenance of protein location in cell / entry of viral genome into host nucleus through nuclear pore complex via importin / miRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / miRNA-mediated gene silencing by inhibition of translation / endoderm development / NLS-dependent protein nuclear import complex ...Post-transcriptional silencing by small RNAs / Transcriptional regulation by small RNAs / Sensing of DNA Double Strand Breaks / maintenance of protein location in cell / entry of viral genome into host nucleus through nuclear pore complex via importin / miRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / miRNA-mediated gene silencing by inhibition of translation / endoderm development / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / RISC complex / regulatory ncRNA-mediated gene silencing / nuclear import signal receptor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / cellular response to starvation / P-body / cytoplasmic stress granule / protein import into nucleus / host cell / molecular adaptor activity / DNA-binding transcription factor binding / postsynaptic density / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / RNA binding / nucleoplasm / cytosol
Similarity search - Function
TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / : / Argonaute hook / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / : / Argonaute hook / 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 / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Trinucleotide repeat-containing gene 6A protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaston, J. / Stewart, A.G. / Christie, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100608 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1090408 Australia
CitationJournal: PLoS ONE / Year: 2017
Title: Structural characterisation of TNRC6A nuclear localisation signal in complex with importin-alpha.
Authors: Chaston, J.J. / Stewart, A.G. / Christie, M.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
B: Importin subunit alpha-1
E: TNRC6A
D: TNRC6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4957
Polymers58,1273
Non-polymers3684
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.791, 89.980, 99.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAs per the authors the biological assembly is a dimer, the second peptide bound is an artifact of the purification/crystallisation process

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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: 55121.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-528
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 TNRC6A


Mass: 1502.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UHK8*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate, Hepes 7.0, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→59.28 Å / Num. obs: 56250 / % possible obs: 100 % / Redundancy: 6.9 % / Rpim(I) all: 0.032 / Net I/σ(I): 19.8
Reflection shellRpim(I) all: 0.377

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJN

1pjn


Resolution: 1.9→44.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 18.11
RfactorNum. reflection% reflection
Rfree0.1816 2666 4.73 %
Rwork0.1516 --
obs0.153 386273 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 24 406 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163572
X-RAY DIFFRACTIONf_angle_d1.2444892
X-RAY DIFFRACTIONf_dihedral_angle_d16.8572230
X-RAY DIFFRACTIONf_chiral_restr0.095590
X-RAY DIFFRACTIONf_plane_restr0.008629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.29011450.25773439X-RAY DIFFRACTION100
1.9216-1.94420.28911720.24113364X-RAY DIFFRACTION100
1.9442-1.96790.25141830.23193441X-RAY DIFFRACTION100
1.9679-1.99280.25791810.22363399X-RAY DIFFRACTION100
1.9928-2.0190.25141680.21243420X-RAY DIFFRACTION100
2.019-2.04670.27241420.193397X-RAY DIFFRACTION100
2.0467-2.07590.21451810.17883430X-RAY DIFFRACTION100
2.0759-2.10690.23751950.18353343X-RAY DIFFRACTION100
2.1069-2.13980.19521780.16483430X-RAY DIFFRACTION100
2.1398-2.17490.20321620.1663405X-RAY DIFFRACTION100
2.1749-2.21240.21571660.16533410X-RAY DIFFRACTION100
2.2124-2.25270.15781470.15833469X-RAY DIFFRACTION100
2.2527-2.2960.18661530.15093436X-RAY DIFFRACTION100
2.296-2.34290.16512110.1443354X-RAY DIFFRACTION100
2.3429-2.39380.18581840.14753430X-RAY DIFFRACTION100
2.3938-2.44950.18631530.14423377X-RAY DIFFRACTION100
2.4495-2.51070.18451510.14353422X-RAY DIFFRACTION100
2.5107-2.57860.19931860.14953402X-RAY DIFFRACTION100
2.5786-2.65450.18251640.15423419X-RAY DIFFRACTION100
2.6545-2.74010.17911600.15123419X-RAY DIFFRACTION100
2.7401-2.83810.17561800.14633411X-RAY DIFFRACTION100
2.8381-2.95170.18121450.14933417X-RAY DIFFRACTION100
2.9517-3.0860.17311600.1573444X-RAY DIFFRACTION100
3.086-3.24860.181770.15623408X-RAY DIFFRACTION100
3.2486-3.45210.21661700.15643425X-RAY DIFFRACTION100
3.4521-3.71850.17691700.14193404X-RAY DIFFRACTION100
3.7185-4.09250.16141950.1273375X-RAY DIFFRACTION100
4.0925-4.68420.1381780.1173402X-RAY DIFFRACTION100
4.6842-5.89950.1391620.15033406X-RAY DIFFRACTION100
5.8995-45.00270.18981590.14763407X-RAY DIFFRACTION99
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)
10.74350.58770.38780.29980.26560.32310.09580.0271-0.11890.0404-0.00320.0023-0.0359-0.00490.00210.18370.01330.01110.1733-0.0140.172739.314373.65757.9052
20.2476-0.07220.06620.0652-0.06090.15450.22240.6646-0.3555-0.42370.1728-0.21080.19630.43510.34290.41110.02770.14790.7171-0.24330.350531.963249.581621.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 72 through 409)
2X-RAY DIFFRACTION2(chain 'B' and resid 410 through 497)

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