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- PDB-8tuv: Merkel Cell Polyomavirus LTA NLSm bound to importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8tuv
TitleMerkel Cell Polyomavirus LTA NLSm bound to importin alpha 2
Components
  • 30S ribosomal protein S11
  • Importin subunit alpha-1
  • SER-ARG-LYS-ARG-LYS-PHE
KeywordsTRANSPORT PROTEIN / importin / karyopherin / nuclear / nls
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 ...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 / Ribosomal protein S11, bacterial-type / Armadillo-like helical / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / Ribosomal protein S11 / Ribosomal protein S11 superfamily / Armadillo-type fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS11 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
Merkel cell polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCross, E.M. / Forwood, J.K. / Alvisi, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin alpha-dependent nuclear localization signals.
Authors: Cross, E.M. / Akbari, N. / Ghassabian, H. / Hoad, M. / Pavan, S. / Ariawan, D. / Donnelly, C.M. / Lavezzo, E. / Petersen, G.F. / Forwood, J.K. / Alvisi, G.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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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: SER-ARG-LYS-ARG-LYS-PHE
C: 30S ribosomal protein S11


Theoretical massNumber of molelcules
Total (without water)70,4103
Polymers70,4103
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.273, 89.516, 97.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 55268.473 Da / Num. of mol.: 1
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 SER-ARG-LYS-ARG-LYS-PHE


Mass: 1270.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Merkel cell polyomavirus
#3: Protein 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.75 M sodium citrate, 0.1 M HEPES pH 6.5, 0.01 M DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→29.89 Å / Num. obs: 30660 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 43.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2 / Num. unique obs: 2946 / CC1/2: 0.72 / Rpim(I) all: 0.42 / Rrim(I) all: 1.14

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.89 Å / SU ML: 0.2592 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 1612 5.27 %
Rwork0.1914 28982 -
obs0.1929 30594 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 116 3474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223427
X-RAY DIFFRACTIONf_angle_d0.50884662
X-RAY DIFFRACTIONf_chiral_restr0.036560
X-RAY DIFFRACTIONf_plane_restr0.0046595
X-RAY DIFFRACTIONf_dihedral_angle_d16.56851269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.32621120.2532404X-RAY DIFFRACTION99.96
2.37-2.440.24111340.2312366X-RAY DIFFRACTION99.92
2.44-2.530.24241180.22212380X-RAY DIFFRACTION99.92
2.53-2.630.28931320.2382402X-RAY DIFFRACTION99.96
2.63-2.750.2611310.22162390X-RAY DIFFRACTION99.96
2.75-2.90.24371380.20512383X-RAY DIFFRACTION99.96
2.9-3.080.25331600.22152378X-RAY DIFFRACTION99.96
3.08-3.320.25631450.2252391X-RAY DIFFRACTION100
3.32-3.650.22771150.19952430X-RAY DIFFRACTION99.96
3.65-4.180.20591450.17092421X-RAY DIFFRACTION100
4.18-5.260.18531370.15662468X-RAY DIFFRACTION100
5.26-29.890.17171450.16912569X-RAY DIFFRACTION99.89

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