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- PDB-5u5r: Crystal Structure and X-ray Diffraction Data Collection of Import... -

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Basic information

Entry
Database: PDB / ID: 5u5r
TitleCrystal Structure and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a PMS2 NLS Peptide
Components
  • Importin subunit alpha-1
  • Mismatch repair endonuclease PMS2
KeywordsTRANSPORT PROTEIN / Nuclear transport / Importin-alpha / PMS2 / NLS
Function / homology
Function and homology information


single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / Sensing of DNA Double Strand Breaks / positive regulation of isotype switching to IgG isotypes / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle ...single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / Sensing of DNA Double Strand Breaks / positive regulation of isotype switching to IgG isotypes / 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 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / nuclear import signal receptor activity / ATP-dependent DNA damage sensor activity / mismatch repair / somatic hypermutation of immunoglobulin genes / TP53 Regulates Transcription of DNA Repair Genes / cytoplasmic stress granule / protein import into nucleus / host cell / endonuclease activity / DNA-binding transcription factor binding / Hydrolases; Acting on ester bonds / postsynaptic density / response to xenobiotic stimulus / glutamatergic synapse / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms ...MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Importin subunit alpha-1 / Mismatch repair endonuclease PMS2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBarros, A.C. / Takeda, A.A. / Dreyer, T.R. / Velazquez-Campoy, A. / Kobe, B. / Fontes, M.R.
CitationJournal: Biochimie / Year: 2018
Title: DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway.
Authors: de Barros, A.C. / Takeda, A.A.S. / Dreyer, T.R. / Velazquez-Campoy, A. / Kobe, B. / Fontes, M.R.M.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
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
A: Importin subunit alpha-1
B: Mismatch repair endonuclease PMS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8663
Polymers56,7122
Non-polymers1541
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-8 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.124, 89.544, 97.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 55330.566 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 Mismatch repair endonuclease PMS2 / DNA mismatch repair protein PMS2 / PMS1 protein homolog 2


Mass: 1381.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P54278, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.600-0.625 M sodium citrate (pH 6) and 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 39804 / % possible obs: 99.7 % / Redundancy: 2.9 % / Net I/σ(I): 18.56

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1Q1S

1q1s


Resolution: 2.1→24.26 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.207 2001 5.03 %
Rwork0.1739 --
obs0.1756 39799 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 8 332 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083375
X-RAY DIFFRACTIONf_angle_d0.9534606
X-RAY DIFFRACTIONf_dihedral_angle_d12.5742056
X-RAY DIFFRACTIONf_chiral_restr0.05562
X-RAY DIFFRACTIONf_plane_restr0.005589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0995-2.1520.36591350.28042615X-RAY DIFFRACTION98
2.152-2.21010.26251500.23172632X-RAY DIFFRACTION99
2.2101-2.27510.23191400.18722682X-RAY DIFFRACTION100
2.2751-2.34850.21281530.18332648X-RAY DIFFRACTION100
2.3485-2.43240.22331310.18172687X-RAY DIFFRACTION100
2.4324-2.52970.24921330.18172674X-RAY DIFFRACTION100
2.5297-2.64470.19581440.18122699X-RAY DIFFRACTION100
2.6447-2.78390.21961210.18052705X-RAY DIFFRACTION100
2.7839-2.9580.24021250.18892716X-RAY DIFFRACTION100
2.958-3.1860.2221600.18432693X-RAY DIFFRACTION100
3.186-3.50570.18951510.17582704X-RAY DIFFRACTION100
3.5057-4.01110.18491540.15412715X-RAY DIFFRACTION100
4.0111-5.0460.1731410.14362768X-RAY DIFFRACTION100
5.046-24.26110.19941630.16752860X-RAY DIFFRACTION99

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