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- PDB-6wbb: Structure of Mouse Importin alpha - MLH1-E475A NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 6wbb
TitleStructure of Mouse Importin alpha - MLH1-E475A NLS peptide complex
Components
  • DNA mismatch repair protein Mlh1
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT/NUCLEAR PROTEIN / Importin alpha / NLS / nuclear import / MLH1 / PROTEIN TRANSPORT / PROTEIN TRANSPORT-NUCLEAR PROTEIN complex
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 / meiotic spindle midzone assembly / MutLalpha complex / 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 / meiotic spindle midzone assembly / MutLalpha complex / 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 / entry of viral genome into host nucleus through nuclear pore complex via importin / synaptonemal complex / female meiosis chromosome segregation / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / ATP-dependent DNA damage sensor activity / 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 / double-strand break repair via nonhomologous end joining / cytoplasmic stress granule / 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: 2.663 Å
AuthorsDe Barros, A.C. / Da Silva, T.D. / Oliveira, H.C. / 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 26, 2020Deposition 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
I: Importin subunit alpha-1
C: DNA mismatch repair protein Mlh1
B: DNA mismatch repair protein Mlh1


Theoretical massNumber of molelcules
Total (without water)52,5443
Polymers52,5443
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.268, 90.556, 100.420
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 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
#2: Protein/peptide DNA mismatch repair protein Mlh1 / MutL protein homolog 1


Mass: 1328.462 Da / Num. of mol.: 2 / Fragment: NLS peptide / Mutation: E475A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40692
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate (pH 6), 10 mM DTT, 0.55 M sodium citrate

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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: 2.663→43.912 Å / Num. obs: 274753 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 53.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.04319 / Rrim(I) all: 0.1572 / Net I/σ(I): 19
Reflection shellResolution: 2.663→2.758 Å / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 27323 / CC1/2: 0.803 / Rpim(I) all: 0.3161 / Rrim(I) all: 1.167

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5P

5u5p


Resolution: 2.663→43.912 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.78
RfactorNum. reflection% reflection
Rfree0.2268 3743 9.51 %
Rwork0.1826 --
obs0.1869 39367 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.84 Å2 / Biso mean: 53.743 Å2 / Biso min: 23.1 Å2
Refinement stepCycle: final / Resolution: 2.663→43.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 70 3470
Biso mean---45.52 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033460
X-RAY DIFFRACTIONf_angle_d0.6574706
X-RAY DIFFRACTIONf_dihedral_angle_d2.7322109
X-RAY DIFFRACTIONf_chiral_restr0.041561
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 (%)
2.6633-2.6970.36721340.3055128496
2.697-2.73250.30341410.27081322100
2.7325-2.76990.31331410.24651324100
2.7699-2.80950.28291390.2461296100
2.8095-2.85140.25171430.24211330100
2.8514-2.8960.28951380.24491319100
2.896-2.94350.31681370.24421323100
2.9435-2.99420.29361380.24641357100
2.9942-3.04860.27941330.24071287100
3.0486-3.10730.26081450.23771341100
3.1073-3.17070.25641370.21181302100
3.1707-3.23960.27841470.20551347100
3.2396-3.31490.28531370.2131306100
3.3149-3.39780.28681380.20471337100
3.3978-3.48960.2511390.21221308100
3.4896-3.59230.24281370.2021312100
3.5923-3.70810.23981410.18951340100
3.7081-3.84060.20081400.17431300100
3.8406-3.99430.21971430.15191344100
3.9943-4.17590.1851340.15181314100
4.1759-4.39590.2131380.1341337100
4.3959-4.6710.18811380.14681303100
4.671-5.03120.19121390.14391348100
5.0312-5.53660.18511370.16321305100
5.5366-6.33580.2591350.18221322100
6.3358-7.97460.18451410.15821331100
7.9746-43.9120.13221330.1261128597
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)
11.34750.4313-0.07092.22420.74230.61530.0914-0.030.0274-0.0282-0.0118-0.002-0.095-0.0371-0.05460.33240.0330.01310.31550.0140.230343.532784.687365.8674
21.65140.56321.04761.86160.61581.56560.08470.4845-0.2107-0.26330.1273-0.36990.11860.3213-0.18990.33970.02380.0240.438-0.08360.437832.29554.06236.2904
33.6727-0.7464-0.36640.94310.53622.71750.12550.1877-0.56480.02060.4316-0.9837-0.13090.4363-0.33270.5167-0.03140.00420.5524-0.17020.711442.851255.500341.692
43.36651.42430.91914.07040.50473.9339-0.0392-0.16-0.1067-0.1095-0.39980.4770.0842-0.26960.14870.37130.03340.03410.4442-0.07680.339336.901684.393958.4615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and (resid 72 through 278 )I72 - 278
2X-RAY DIFFRACTION2chain 'I' and (resid 279 through 497 )I279 - 497
3X-RAY DIFFRACTION3chain 'C' and (resid 467 through 474 )C467 - 474
4X-RAY DIFFRACTION4chain 'B' and (resid 467 through 476 )B467 - 476

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