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- PDB-5u5p: Crystal Structure and X-ray Diffraction Data Collection of Import... -

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Basic information

Entry
Database: PDB / ID: 5u5p
TitleCrystal Structure and X-ray Diffraction Data Collection of Importin-alpha from Mus Musculus Complexed with a MLH1 NLS Peptide
Components
  • DNA mismatch repair protein Mlh1
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Nuclear transport / Importin-alpha / MLH1 / NLS
Function / homology
Function and homology information


chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / MutLalpha complex / meiotic spindle midzone assembly / guanine/thymine mispair binding ...chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / MutLalpha complex / meiotic spindle midzone assembly / guanine/thymine mispair binding / meiotic telomere clustering / positive regulation of isotype switching to IgA isotypes / nuclear-transcribed mRNA poly(A) tail shortening / resolution of meiotic recombination intermediates / homologous chromosome pairing at meiosis / Sensing of DNA Double Strand Breaks / positive regulation of isotype switching to IgG isotypes / synaptonemal complex / entry of viral genome into host nucleus through nuclear pore complex via importin / female meiosis chromosome segregation / positive regulation of viral life cycle / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / ATP-dependent DNA damage sensor activity / nuclear localization sequence binding / oogenesis / NLS-bearing protein import into nucleus / somatic hypermutation of immunoglobulin genes / mismatch repair / host cell / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / response to bacterium / Meiotic recombination / cytoplasmic stress granule / double-strand break repair via nonhomologous end joining / protein import into nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome / spermatogenesis / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / 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 ...DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / 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 / DNA mismatch repair protein Mlh1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.171 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 15, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
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
C: DNA mismatch repair protein Mlh1
B: DNA mismatch repair protein Mlh1
A: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0844
Polymers57,9293
Non-polymers1541
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint4 kcal/mol
Surface area18110 Å2
Unit cell
Length a, b, c (Å)77.215, 89.071, 99.139
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/peptide DNA mismatch repair protein Mlh1 / / MutL protein homolog 1


Mass: 1299.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40692
#2: 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 / Fragment: residues 70-529
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
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


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


Mass: 18.015 Da / Num. of mol.: 224 / 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: 58.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.600-0.625 M sodium citrate (pH 6) 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: 2.17→40 Å / Num. obs: 36607 / % possible obs: 99.5 % / Redundancy: 6.4 % / Net I/σ(I): 24.11

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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: 2.171→38.579 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.44
RfactorNum. reflection% reflection
Rfree0.2108 1827 4.99 %
Rwork0.1815 --
obs0.183 36597 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.171→38.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 8 224 3635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083479
X-RAY DIFFRACTIONf_angle_d1.0324732
X-RAY DIFFRACTIONf_dihedral_angle_d15.3292123
X-RAY DIFFRACTIONf_chiral_restr0.06565
X-RAY DIFFRACTIONf_plane_restr0.005608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1707-2.22940.29941430.26922535X-RAY DIFFRACTION97
2.2294-2.2950.26291230.23432631X-RAY DIFFRACTION98
2.295-2.36910.27351290.22862649X-RAY DIFFRACTION99
2.3691-2.45370.24571260.20212649X-RAY DIFFRACTION100
2.4537-2.5520.2271280.1932658X-RAY DIFFRACTION99
2.552-2.66810.22361660.19922627X-RAY DIFFRACTION100
2.6681-2.80870.22141350.19172662X-RAY DIFFRACTION100
2.8087-2.98460.24321340.20362685X-RAY DIFFRACTION100
2.9846-3.2150.24071420.19312691X-RAY DIFFRACTION100
3.215-3.53830.2151380.1832681X-RAY DIFFRACTION100
3.5383-4.04980.19571510.15832729X-RAY DIFFRACTION100
4.0498-5.10050.18191550.15562724X-RAY DIFFRACTION100
5.1005-38.58460.17731570.16612849X-RAY DIFFRACTION100

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