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- PDB-6wbc: Structure of Mouse Importin alpha- MLH1-R472K NLS Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 6wbc
TitleStructure of Mouse Importin alpha- MLH1-R472K NLS Peptide Complex
Components
  • DNA mismatch repair protein Mlh1
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT/NUCLEAR PROTEIN / Importin alpha / Nuclear import / NLS / 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 / 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 / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of isotype switching to IgA isotypes / Sensing of DNA Double Strand Breaks / resolution of meiotic recombination intermediates / homologous chromosome pairing at meiosis / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of isotype switching to IgG isotypes / female meiosis chromosome segregation / synaptonemal complex / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / nuclear import signal receptor activity / oogenesis / ATP-dependent DNA damage sensor activity / mismatch repair / somatic hypermutation of immunoglobulin genes / male germ cell nucleus / response to bacterium / TP53 Regulates Transcription of DNA Repair Genes / enzyme activator activity / double-strand break repair via nonhomologous end joining / Meiotic recombination / intrinsic apoptotic signaling pathway in response to DNA damage / protein import into nucleus / cytoplasmic stress granule / host cell / chromosome / spermatogenesis / DNA-binding transcription factor binding / postsynaptic density / chromatin binding / glutamatergic synapse / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / membrane / 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: 2.15 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
A: Importin subunit alpha-1
B: DNA mismatch repair protein Mlh1


Theoretical massNumber of molelcules
Total (without water)51,2452
Polymers51,2452
Non-polymers00
Water4,396244
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)78.697, 90.229, 100.077
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: 1358.484 Da / Num. of mol.: 1 / Fragment: NLS peptide / Mutation: R472K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40692
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate (pH 6), 0.575 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: 2.15→46.76 Å / Num. obs: 514128 / % possible obs: 99.76 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08643 / Rpim(I) all: 0.0246 / Rrim(I) all: 0.08643 / Net I/σ(I): 24.4
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 1.753 / Num. unique obs: 50867 / CC1/2: 0.842 / Rpim(I) all: 0.4939 / Rrim(I) all: 1.822 / % possible all: 99.36

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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: 2.15→45.114 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.93
RfactorNum. reflection% reflection
Rfree0.2126 3781 5.06 %
Rwork0.1801 --
obs0.1817 74739 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.74 Å2 / Biso mean: 51.4382 Å2 / Biso min: 22.76 Å2
Refinement stepCycle: final / Resolution: 2.15→45.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 244 3550
Biso mean---52.51 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043365
X-RAY DIFFRACTIONf_angle_d0.7024583
X-RAY DIFFRACTIONf_dihedral_angle_d4.742044
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.2270.27511400.2769263398
2.177-2.20560.36011340.3433256199
2.2056-2.23580.36131390.32172651100
2.2358-2.26780.43311430.3865263199
2.2678-2.30160.30271430.27922619100
2.3016-2.33760.21461410.2248260499
2.3376-2.37590.25011410.22252652100
2.3759-2.41690.24831340.20472590100
2.4169-2.46080.25371450.19372629100
2.4608-2.50810.24391400.18422646100
2.5081-2.55930.2421430.1922665100
2.5593-2.6150.2191340.19512584100
2.615-2.67580.20241430.18252663100
2.6758-2.74270.24051400.18882634100
2.7427-2.81680.24081460.18782605100
2.8168-2.89970.23591410.1892645100
2.8997-2.99330.20031460.18742632100
2.9933-3.10030.26461310.18912633100
3.1003-3.22430.24251410.1862640100
3.2243-3.3710.24141390.18222632100
3.371-3.54870.19271410.17962660100
3.5487-3.77090.22821370.16462609100
3.7709-4.06190.15191400.14312631100
4.0619-4.47040.14311400.13532639100
4.4704-5.11650.19011390.1462618100
5.1165-6.44320.17791420.17182657100
6.4432-45.1140.17541380.1475259599
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)
12.4495-0.4961-0.58585.252.09691.930.173-0.04880.2371-0.1602-0.04990.0172-0.2555-0.1378-0.12330.3175-0.0010.04730.312-0.00210.263546.018693.060865.7919
21.95920.78910.74022.17170.62851.95390.12810.0103-0.33770.1109-0.02860.0090.0716-0.0181-0.13560.25860.0018-0.01060.25010.01890.332138.536266.739261.827
32.6030.47941.29853.73330.84732.9210.05920.8033-0.2794-0.5470.2171-0.66830.03450.5872-0.1430.31960.00730.07850.5232-0.13850.487431.215652.276131.9133
46.8699-3.2019-3.02736.78165.8215.4859-0.28280.0888-1.1299-0.6177-0.77881.87130.0636-0.43250.63710.44870.03150.00440.4783-0.02770.578336.843584.658758.212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 202 )A72 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 322 )A203 - 322
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 497 )A323 - 497
4X-RAY DIFFRACTION4chain 'B' and (resid 467 through 476 )B467 - 476

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