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- PDB-3tj3: Structure of importin a5 bound to the N-terminus of Nup50 -

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Basic information

Entry
Database: PDB / ID: 3tj3
TitleStructure of importin a5 bound to the N-terminus of Nup50
Components
  • Importin subunit alpha-1
  • Nuclear pore complex protein Nup50
KeywordsPROTEIN TRANSPORT / ARMADILLO repeat / nuclear import adaptor / NLS-bearing proteins / nucleo-cytoplasmic shuttling
Function / homology
Function and homology information


satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / Inhibition of nitric oxide production / regulation of DNA recombination / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / Inhibition of nitric oxide production / regulation of DNA recombination / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / SUMOylation of SUMOylation proteins / postsynapse to nucleus signaling pathway / Apoptosis induced DNA fragmentation / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of canonical Wnt signaling pathway / nucleocytoplasmic transport / nuclear import signal receptor activity / Viral Messenger RNA Synthesis / nuclear localization sequence binding / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / Integration of provirus / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Interferon alpha/beta signaling / nuclear envelope / snRNP Assembly / nuclear membrane / regulation of apoptotic process / postsynaptic density / glutamatergic synapse / dendrite / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding domain / Ran binding protein RanBP1-like / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding domain / Ran binding protein RanBP1-like / 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 / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / 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-5 / Nuclear pore complex protein Nup50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsPumroy, R. / Nardozzi, J.D. / Hart, D.J. / Root, M.J. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Nucleoporin Nup50 stabilizes closed conformation of armadillo repeat 10 in importin alpha 5.
Authors: Pumroy, R.A. / Nardozzi, J.D. / Hart, D.J. / Root, M.J. / Cingolani, G.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
C: Nuclear pore complex protein Nup50
B: Importin subunit alpha-1
D: Nuclear pore complex protein Nup50


Theoretical massNumber of molelcules
Total (without water)122,4154
Polymers122,4154
Non-polymers00
Water2,342130
1
A: Importin subunit alpha-1
C: Nuclear pore complex protein Nup50


Theoretical massNumber of molelcules
Total (without water)61,2072
Polymers61,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-5 kcal/mol
Surface area21350 Å2
MethodPISA
2
B: Importin subunit alpha-1
D: Nuclear pore complex protein Nup50


Theoretical massNumber of molelcules
Total (without water)61,2072
Polymers61,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-5 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.683, 98.291, 135.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 82:459 or resseq 466:506 )
211chain B and (resseq 82:459 or resseq 466:506 )
112chain C and (resseq 0:18 or resseq 23:46 )
212chain D and (resseq 0:18 or resseq 23:46 )

NCS ensembles :
ID
1
2
DetailsTHE QUATERNARY STRUCTURE IS A HETERODIMER OF IMPORTIN A5 AND NUP50.

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Components

#1: Protein Importin subunit alpha-1 / importin alpha 5 / Karyopherin subunit alpha-1 / Nucleoprotein interactor 1 / NPI-1 / RAG cohort ...importin alpha 5 / Karyopherin subunit alpha-1 / Nucleoprotein interactor 1 / NPI-1 / RAG cohort protein 2 / SRP1-beta


Mass: 49401.328 Da / Num. of mol.: 2 / Fragment: UNP residues 66-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA1, RCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52294
#2: Protein Nuclear pore complex protein Nup50 / 50 kDa nucleoporin / Nuclear pore-associated protein 60 kDa-like / Nucleoporin Nup50


Mass: 11806.040 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-109)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP50, NPAP60L, PRO1146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKX7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.976
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 20, 2011
DECTRIS PILATUS 6M2PIXELApr 15, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
21.11
ReflectionResolution: 2.7→79.532 Å / Num. all: 29294 / Num. obs: 29294 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.086 / Net I/σ(I): 26.86
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.15 / Num. unique all: 2820 / Rsym value: 0.618 / % possible all: 94.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JDQ

2jdq


Resolution: 2.702→15.028 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1350 5 %RANDOM
Rwork0.2149 ---
all0.217 ---
obs0.217 26999 88.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.132 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.2301 Å20 Å20 Å2
2---0.0863 Å2-0 Å2
3---11.3164 Å2
Refinement stepCycle: LAST / Resolution: 2.702→15.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7415 0 0 130 7545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057517
X-RAY DIFFRACTIONf_angle_d0.79510189
X-RAY DIFFRACTIONf_dihedral_angle_d15.7492795
X-RAY DIFFRACTIONf_chiral_restr0.0521189
X-RAY DIFFRACTIONf_plane_restr0.0031313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3254X-RAY DIFFRACTIONPOSITIONAL
12B3254X-RAY DIFFRACTIONPOSITIONAL0.028
21C352X-RAY DIFFRACTIONPOSITIONAL
22D352X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.702-2.79810.36841040.35092027X-RAY DIFFRACTION71
2.7981-2.90940.41911200.34022213X-RAY DIFFRACTION78
2.9094-3.04070.39521270.31532317X-RAY DIFFRACTION81
3.0407-3.19960.31941320.29022518X-RAY DIFFRACTION89
3.1996-3.39790.36111390.26952731X-RAY DIFFRACTION95
3.3979-3.65680.28411420.25322739X-RAY DIFFRACTION95
3.6568-4.01840.22421410.20542650X-RAY DIFFRACTION93
4.0184-4.58530.2031400.16542671X-RAY DIFFRACTION92
4.5853-5.72340.21721480.17442840X-RAY DIFFRACTION97
5.7234-15.02830.19391570.16342943X-RAY DIFFRACTION97
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)
12.89370.9047-0.24816.0222-2.11913.306-0.2591-0.1673-0.31460.43120.1374-0.259-0.14350.0120.08180.333-0.0022-0.12270.1597-0.03670.201521.62017.8822-20.4581
22.66241.7361-0.15187.3589-0.1271.3797-0.34150.60120.1441-0.89760.39420.2557-0.02990.0624-0.02810.5087-0.14470.05420.55680.0310.324412.1008-26.2877-19.5491
36.4314-2.72430.11961.784-0.79964.484-0.1642-0.4648-0.5114-0.10230.2241-0.16160.4355-0.0043-0.14040.6095-0.07160.21770.4215-0.12140.598125.8628-53.4049-10.3664
49.322-1.7133-3.47550.95271.19091.7734-0.49550.42541.39990.56450.71721.9989-0.4566-0.2858-1.26250.69280.17730.21481.9218-0.22591.139512.7962-42.0755-1.0021
54.59871.9679-4.45313.5572-0.95754.68110.1539-1.0405-0.19590.9237-0.03540.0690.50690.41630.00440.6875-0.14650.05370.58810.12850.337318.2447-33.359-9.119
69.1817-1.48641.7942.0691-2.69299.0488-0.10761.293-0.1279-0.89720.058-1.07990.66560.68940.83020.8172-0.12040.11831.02110.08840.615724.4274-20.4846-19.8535
77.733-7.00151.88926.3395-1.75550.5618-0.1171-0.2399-1.07550.64470.30291.47410.2931-1.753-0.38471.3306-0.04690.52441.41510.49311.552332.5263-26.443-24.5239
88.4122-3.1280.09679.4608-0.98846.43950.2918-0.16640.29010.9401-0.1166-1.315-0.8480.92580.55930.6123-0.26110.22570.7533-0.24351.20943.7651-46.271-5.626
90.62350.64961.26755.08453.55179.11590.82430.628-0.30461.31390.5177-1.45051.31780.9864-1.2410.73090.2640.1950.9636-0.11231.138936.1464-62.9098-5.8441
105.9887-2.84120.07674.19120.4622.9666-0.3127-0.76041.2170.32520.2093-0.3768-0.597-0.14710.02340.77030.0206-0.26680.457-0.06740.823514.71216.750422.2687
111.6844-0.3222-0.16896.0341.7191.421-0.16960.0758-0.0148-0.31430.1888-0.17510.26740.1024-0.00340.31840.02760.03690.3582-0.01780.227824.2707-27.304119.4064
125.55272.7031.54063.59040.44783.6292-0.28730.2381-0.6560.27260.16270.21390.23050.0780.01730.58030.04530.1940.23640.09880.456114.1863-50.440111.3938
139.1278-2.36581.22784.7264-0.57697.72580.26240.4794-0.7719-0.58350.11260.2010.6033-0.1637-0.26160.5762-0.04550.15950.2890.03940.60275.6056-57.74145.1099
145.9817-0.31173.01290.1550.00341.7067-0.60180.49411.1264-0.2531-0.4715-0.3207-0.3058-1.1725-0.03150.91030.06920.43121.68910.11151.262423.516-41.9266-0.1856
152.316-2.4587-3.83275.26363.68546.4343-1.0530.11660.0438-1.0725-0.75510.97990.285-0.96370.22821.38450.1049-0.11910.5485-0.27760.347718.121-33.82758.4207
161.38562.69592.45125.42984.30558.7869-0.5287-1.73490.5229-1.3607-0.77161.247-1.2111-1.74091.4420.74710.1860.04510.7728-0.18261.153811.9823-21.622219.9358
172.43611.79921.29793.90782.2131.8160.2522-0.23681.68160.9489-0.04650.05980.21220.3148-0.71461.6668-0.36080.74140.8209-0.44352.35383.3854-28.677523.7102
185.46484.84263.68229.49992.67414.14311.8679-0.97351.21521.4217-0.5397-0.0788-2.198-0.284-0.91191.2087-0.0690.82560.56750.07261.5523-1.6295-40.475216.5879
199.30012.29620.20632.0816-0.38418.48460.71492.64790.6551-0.6183-0.68182.1089-0.0148-0.71480.28810.9960.4448-0.2110.9262-0.00021.0932-9.3298-48.4276-0.1075
206.8628-0.1296-2.17441.2136-1.93365.84260.7653-0.5941-0.7471-1.228-0.98540.4951.51680.86250.13010.91150.08230.24510.47040.10121.0015-0.2385-62.72682.7814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 82:225)
2X-RAY DIFFRACTION2chain 'A' and (resseq 226:393)
3X-RAY DIFFRACTION3chain 'A' and (resseq 394:508)
4X-RAY DIFFRACTION4chain 'C' and (resseq -3:1)
5X-RAY DIFFRACTION5chain 'C' and (resseq 2:6)
6X-RAY DIFFRACTION6chain 'C' and (resseq 7:16)
7X-RAY DIFFRACTION7chain 'C' and (resseq 17:21)
8X-RAY DIFFRACTION8chain 'C' and (resseq 22:37)
9X-RAY DIFFRACTION9chain 'C' and (resseq 38:47)
10X-RAY DIFFRACTION10chain 'B' and (resseq 82:225)
11X-RAY DIFFRACTION11chain 'B' and (resseq 226:393)
12X-RAY DIFFRACTION12chain 'B' and (resseq 394:460)
13X-RAY DIFFRACTION13chain 'B' and (resseq 461:507)
14X-RAY DIFFRACTION14chain 'D' and (resseq -3:1)
15X-RAY DIFFRACTION15chain 'D' and (resseq 2:6)
16X-RAY DIFFRACTION16chain 'D' and (resseq 7:16)
17X-RAY DIFFRACTION17chain 'D' and (resseq 17:21)
18X-RAY DIFFRACTION18chain 'D' and (resseq 22:26)
19X-RAY DIFFRACTION19chain 'D' and (resseq 27:37)
20X-RAY DIFFRACTION20chain 'D' and (resseq 38:46)

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