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- PDB-7n9h: Structure of the mammalian importin a1 bound to the TDP-43 NLS -

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Basic information

Entry
Database: PDB / ID: 7n9h
TitleStructure of the mammalian importin a1 bound to the TDP-43 NLS
Components
  • Importin subunit alpha-1
  • TAR DNA-binding protein 43
KeywordsPROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA / NLS / TDP-43
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / nuclear inner membrane organization / regulation of DNA recombination / interchromatin granule / perichromatin fibrils / entry of viral genome into host nucleus through nuclear pore complex via importin / 3'-UTR-mediated mRNA destabilization / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex ...Sensing of DNA Double Strand Breaks / nuclear inner membrane organization / regulation of DNA recombination / interchromatin granule / perichromatin fibrils / entry of viral genome into host nucleus through nuclear pore complex via importin / 3'-UTR-mediated mRNA destabilization / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / DNA metabolic process / 3'-UTR-mediated mRNA stabilization / CaMK IV-mediated phosphorylation of CREB / intracellular non-membrane-bounded organelle / nuclear localization sequence binding / NLS-bearing protein import into nucleus / negative regulation by host of viral transcription / positive regulation of type I interferon production / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing / molecular condensate scaffold activity / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / regulation of protein stability / positive regulation of insulin secretion / regulation of circadian rhythm / ISG15 antiviral mechanism / histone deacetylase binding / cytoplasmic stress granule / positive regulation of protein import into nucleus / mRNA processing / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / rhythmic process / regulation of gene expression / double-stranded DNA binding / nuclear membrane / regulation of apoptotic process / Estrogen-dependent gene expression / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Golgi membrane / negative regulation of gene expression / lipid binding / endoplasmic reticulum membrane / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-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 ...: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Importin subunit alpha-1 / TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDoll, S.G. / Lokareddy, R.K. / Cingolani, G.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122844 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140733 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA56036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD017987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD023479 United States
CitationJournal: Cell Rep / Year: 2022
Title: Recognition of the TDP-43 nuclear localization signal by importin alpha 1/ beta.
Authors: Doll, S.G. / Meshkin, H. / Bryer, A.J. / Li, F. / Ko, Y.H. / Lokareddy, R.K. / Gillilan, R.E. / Gupta, K. / Perilla, J.R. / Cingolani, G.
History
DepositionJun 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)49,1272
Polymers49,1272
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, equilibrium centrifugation, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint3 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.373, 91.306, 97.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 46386.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52292
#2: Protein/peptide TAR DNA-binding protein 43 / TDP-43


Mass: 2741.172 Da / Num. of mol.: 1
Fragment: Nuclear localization signal motif, residues 79-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13148
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.5M sodium citrate, 10 mM mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36296 / % possible obs: 98.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 37.33 Å2 / CC1/2: 0.995 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3545 / CC1/2: 0.549 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y2A

1y2a


Resolution: 2.2→14.97 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 1994 5.53 %
Rwork0.1896 34087 -
obs0.191 36081 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.34 Å2 / Biso mean: 49.4035 Å2 / Biso min: 25.84 Å2
Refinement stepCycle: final / Resolution: 2.2→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 0 163 3554
Biso mean---47.25 -
Num. residues----445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.28451340.2822353248798
2.25-2.320.32831350.267124222557100
2.32-2.380.29751580.247723832541100
2.38-2.460.26191360.229624162552100
2.46-2.550.25281350.216324062541100
2.55-2.650.27481510.216223942545100
2.65-2.770.2351440.203924312575100
2.77-2.910.2481390.199124232562100
2.91-3.10.261440.202824202564100
3.1-3.330.24471390.198424392578100
3.33-3.660.19861460.1924482594100
3.66-4.180.1761390.160424822621100
4.18-5.230.17611470.162424902637100
5.23-14.970.17341470.166725802727100
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)
11.3859-0.30140.67973.5995-1.11260.86930.0970.0956-0.1556-0.1665-0.037-0.12960.23130.0652-0.00280.3769-0.0003-0.03960.34170.00290.3289-6.1545-93.9734113.1034
20.93140.9118-1.23291.6794-1.78482.49550.07580.04850.03530.1427-0.00530.0601-0.1065-0.0218-0.00010.3171-0.003-0.01630.3215-0.0110.36344.6842-63.1305103.8356
31.3895-0.6248-0.83721.247-0.30881.82350.06780.75160.2034-0.44330.11950.19340.1163-0.44960.00160.48250.0044-0.07470.73640.13430.37546.8644-51.428472.7696
40.61530.3988-0.2740.37480.19081.4019-0.05240.86950.3015-0.2938-0.14490.3642-0.3975-0.5602-0.02060.42480.0388-0.02520.61620.17130.6323-2.7206-55.686589.5315
50.09790.02920.12080.02140.01280.1629-0.05830.0811-0.3027-0.1298-0.54370.14450.6083-0.0826-0.05541.1105-0.27680.03231.04960.03541.3115-1.0051-68.800791.7954
61.82960.80620.56880.37920.46111.8594-0.0438-0.1992-0.0897-0.31240.2581-0.9549-0.27960.9270.01660.62920.10180.06250.77080.03080.95683.0876-85.5971106.3496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 75 through 202 )C75 - 202
2X-RAY DIFFRACTION2chain 'C' and (resid 203 through 390 )C203 - 390
3X-RAY DIFFRACTION3chain 'C' and (resid 391 through 496 )C391 - 496
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 84 )A80 - 84
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 94 )A85 - 94
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 102 )A95 - 102

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