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- PDB-7m60: Structure of Mouse Importin alpha MLH1-S467A NLS Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 7m60
TitleStructure of Mouse Importin alpha MLH1-S467A NLS Peptide Complex
Components
  • DNA mismatch repair protein Mlh1 NLS peptide
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Importin alpha / nuclear import / NLS / MLH1
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 / NLS-bearing protein import into nucleus / oogenesis / somatic hypermutation of immunoglobulin genes / mismatch repair / 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 / host cell / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Armadillo-like helical / Armadillo-type fold / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA mismatch repair protein Mlh1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe Oliveira, H.C. / Da Silva, T.D. / Fukuda, C.A. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Biochem.J. / Year: 2021
Title: Structural and calorimetric studies reveal specific determinants for the binding of a high-affinity NLS to mammalian importin-alpha.
Authors: de Oliveira, H.C. / da Silva, T.D. / Salvador, G.H.M. / Moraes, I.R. / Fukuda, C.A. / de Barros, A.C. / Fontes, M.R.M.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 18, 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 NLS peptide
B: DNA mismatch repair protein Mlh1 NLS peptide
A: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)52,6283
Polymers52,6283
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint7 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.440, 90.049, 99.601
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/peptide DNA mismatch repair protein Mlh1 NLS peptide / MutL protein homolog 1


Mass: 1370.498 Da / Num. of mol.: 2 / Fragment: residues 466-476 / Mutation: S467A / 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: 49886.633 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium citrate pH6, 0.65 M sodium citrate, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 2.3→42.043 Å / Num. obs: 345941 / % possible obs: 98.12 % / Redundancy: 11 % / Biso Wilson estimate: 39.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08764 / Rpim(I) all: 0.02724 / Rrim(I) all: 0.09192 / Net I/σ(I): 24.37
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.9764 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 3024 / CC1/2: 0.862 / Rpim(I) all: 0.2968 / Rrim(I) all: 1.022 / % possible all: 96.31

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5P

5u5p


Resolution: 2.3→42.043 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 2953 4.97 %
Rwork0.1737 56516 -
obs0.1753 59469 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.26 Å2 / Biso mean: 49.4781 Å2 / Biso min: 21.93 Å2
Refinement stepCycle: final / Resolution: 2.3→42.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 0 230 3626
Biso mean---50.21 -
Num. residues----445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033456
X-RAY DIFFRACTIONf_angle_d0.674704
X-RAY DIFFRACTIONf_dihedral_angle_d2.622105
X-RAY DIFFRACTIONf_chiral_restr0.041563
X-RAY DIFFRACTIONf_plane_restr0.004605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.33770.30091330.2666256595
2.3377-2.3780.31171460.2573268797
2.378-2.42130.25671410.2372267298
2.4213-2.46780.31420.2243266598
2.4678-2.51820.33221380.2306264597
2.5182-2.57290.22271450.2119270098
2.5729-2.63280.24241400.2103269298
2.6328-2.69860.24341410.2266398
2.6986-2.77160.23461410.1955271699
2.7716-2.85310.23471390.1952268298
2.8531-2.94520.24851410.1936268498
2.9452-3.05040.23591420.1967271298
3.0504-3.17250.22371420.1864269799
3.1725-3.31680.23161420.1888272399
3.3168-3.49160.19261380.1838269699
3.4916-3.71030.1831370.1637273899
3.7103-3.99650.17381410.1429270399
3.9965-4.39830.15721380.1317272799
4.3983-5.03390.18171400.1388273399
5.0339-6.33870.19461410.16512726100
6.3387-42.0430.17061450.1517269098
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)
16.095-1.4760.67821.9478-0.99255.54720.0290.8816-0.31930.46430.3154-1.1379-0.1290.8757-0.37170.4947-0.0821-0.0850.5962-0.23090.854342.619255.562241.384
24.74040.4241.61653.54453.04597.30770.4510.077-0.6073-0.4268-0.88351.2562-0.2803-0.61830.35870.40970.024-0.00770.4259-0.01740.506136.584384.371657.789
32.2964-0.1093-0.77984.54581.53781.44790.19140.04420.2636-0.1488-0.06770.0018-0.247-0.091-0.12580.32050.01310.03280.3049-0.00230.22945.833993.015965.3927
41.40721.16241.44331.2251.03131.62340.15910.0948-0.35510.14380.0271-0.08990.18580.0666-0.19320.28810.0094-0.02310.2728-0.00940.373336.207662.676156.7844
51.946-0.38830.08672.88950.73222.33390.10760.9047-0.1835-0.72040.1954-0.5154-0.05990.4166-0.17890.5241-0.01660.1040.7793-0.18780.531331.341751.298825.4536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 467 through 475 )C467 - 475
2X-RAY DIFFRACTION2chain 'B' and (resid 467 through 476 )B467 - 476
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 202 )A72 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 375 )A203 - 375
5X-RAY DIFFRACTION5chain 'A' and (resid 376 through 497 )A376 - 497

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