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- PDB-6iu7: Crystal structure of importin-alpha1 bound to the 53BP1 nuclear l... -

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Basic information

Entry
Database: PDB / ID: 6iu7
TitleCrystal structure of importin-alpha1 bound to the 53BP1 nuclear localization signal (wild-type)
Components
  • Importin subunit alpha-1
  • Peptide from TP53-binding protein 1
KeywordsTRANSPORT PROTEIN/PROTEIN BINDING / importin / NLS / TRANSPORT PROTEIN / TRANSPORT PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / Sensing of DNA Double Strand Breaks / positive regulation of isotype switching / histone H4K20me2 reader activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / cellular response to X-ray / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / double-strand break repair via classical nonhomologous end joining ...ubiquitin-modified histone reader activity / Sensing of DNA Double Strand Breaks / positive regulation of isotype switching / histone H4K20me2 reader activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / cellular response to X-ray / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / nuclear import signal receptor activity / telomeric DNA binding / : / histone reader activity / SUMOylation of transcription factors / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of double-strand break repair via homologous recombination / DNA damage checkpoint signaling / replication fork / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / double-strand break repair via nonhomologous end joining / cytoplasmic stress granule / protein import into nucleus / p53 binding / host cell / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / DNA-binding transcription factor binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / postsynaptic density / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) 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 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Ribosomal protein L2, domain 2 / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / TP53-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatsuura, Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural and biochemical characterization of the recognition of the 53BP1 nuclear localization signal by importin-alpha.
Authors: Matsuura, Y.
History
DepositionNov 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: Peptide from TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)48,7522
Polymers48,7522
Non-polymers00
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint6 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.460, 90.150, 96.720
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: 46242.957 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 Peptide from TP53-binding protein 1 / p53BP1


Mass: 2508.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: sodium citrate, HEPES, DTT

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→32.973 Å / Num. obs: 54893 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Net I/σ(I): 8.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.674 / Num. unique obs: 3481 / CC1/2: 0.71 / Rpim(I) all: 0.408 / Rrim(I) all: 0.791 / % possible all: 99

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X8N

5x8n


Resolution: 1.9→32.973 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.51
RfactorNum. reflection% reflection
Rfree0.1851 2746 5.01 %
Rwork0.1535 --
obs0.155 54836 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.42 Å2 / Biso mean: 37.0533 Å2 / Biso min: 14.81 Å2
Refinement stepCycle: final / Resolution: 1.9→32.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 0 316 3711
Biso mean---44.05 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.93280.25151510.22812554270599
1.9328-1.9680.24661530.21072544269799
1.968-2.00580.21031290.19992579270899
2.0058-2.04670.22251530.18652546269999
2.0467-2.09120.17751500.16512591274199
2.0912-2.13990.16851470.15442493264098
2.1399-2.19340.19721130.15472569268297
2.1934-2.25270.17891470.14792562270999
2.2527-2.31890.19861520.140825992751100
2.3189-2.39380.16761290.145325882717100
2.3938-2.47930.19261140.147226252739100
2.4793-2.57850.22041210.1572634275599
2.5785-2.69580.19981300.156425982728100
2.6958-2.83790.1921290.156726402769100
2.8379-3.01560.19911240.16422630275499
3.0156-3.24820.21341270.16262568269597
3.2482-3.57480.18621280.154626592787100
3.5748-4.09120.16211510.132326492800100
4.0912-5.15130.1741320.134127192851100
5.1513-32.9780.15891660.15562743290998
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)
13.3541-0.9024-1.93510.44790.65073.8950.1758-0.0599-0.29640.3943-0.1118-0.04510.31380.2788-0.01450.3278-0.0531-0.07430.2241-0.03410.27196.3859-16.3644-18.0288
23.74450.6250.99173.2646-0.4143.81770.1302-0.404-0.26820.5668-0.08630.19540.0529-0.2603-0.01550.2899-0.05260.00420.1868-0.01690.18343.9191-8.4946-8.9211
31.65360.0661-0.08662.47710.20860.64060.04390.0878-0.0319-0.0843-0.0057-0.02430.1032-0.0091-0.04070.1465-0.0072-0.01630.1378-0.00780.1037.90644.8448-16.8293
41.9342-0.44860.30991.6478-1.14312.65920.03360.0470.0462-0.2472-0.04890.20120.1999-0.02470.0030.17690.017-0.00890.1392-0.00780.1859-1.701616.1867-16.5889
56.0834-1.88335.52523.0335-1.58357.1809-0.03030.17250.4991-0.0891-0.025-0.1619-0.34130.22780.08070.1706-0.03530.02220.16670.01080.26110.452724.8162-12.0313
63.49470.4393-1.06343.8368-0.57543.60890.00870.0799-0.1912-0.3577-0.20630.2150.0323-0.10170.19290.17710.0195-0.04160.17560.00350.1801-7.339522.1677-16.1943
71.4477-1.3058-0.78362.46520.91991.93670.16660.05620.3147-0.2242-0.0149-0.278-0.23170.0144-0.10980.17110.01140.05230.1642-0.00280.2117-3.246930.579-4.9738
82.0934-0.1588-0.77571.95580.73442.15120.0313-0.33690.17410.11940.0464-0.1948-0.01710.1904-0.08010.13260.0021-0.01410.2006-0.04480.1785-10.90335.99812.7293
91.4566-0.5-0.56898.2995-0.63212.85090.098-0.71050.5610.53-0.0492-0.8651-0.16610.783-0.040.3956-0.0439-0.11860.6678-0.20860.4501-4.537942.845824.3236
103.578-0.93850.32354.6153-1.08670.7034-0.1655-1.04710.17381.41590.186-0.3768-0.04830.6203-0.03740.7923-0.0196-0.10390.975-0.11240.3767-5.661939.564633.7146
112.13462.01091.32342.09310.97521.28750.2966-0.4303-0.16440.1121-0.14710.01210.33790.5875-0.30880.28450.0328-0.07690.3555-0.10640.33482.698431.57928.3812
122.00524.22951.45431.30980.40439.81840.0607-0.7088-0.28670.67520.0643-0.31290.59110.1787-0.10330.62130.1975-0.00050.4665-0.02830.49080.292415.71084.991
131.7584-0.30220.32864.46532.91295.07870.1089-0.00590.00280.2879-0.40670.58260.2143-0.55010.19330.1483-0.00540.02720.2263-0.02190.2159-2.10456.8687-7.2201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 75:96)A75 - 96
2X-RAY DIFFRACTION2(chain A and resid 97:123)A97 - 123
3X-RAY DIFFRACTION3(chain A and resid 124:213)A124 - 213
4X-RAY DIFFRACTION4(chain A and resid 214:240)A214 - 240
5X-RAY DIFFRACTION5(chain A and resid 241:254)A241 - 254
6X-RAY DIFFRACTION6(chain A and resid 255:268)A255 - 268
7X-RAY DIFFRACTION7(chain A and resid 269:337)A269 - 337
8X-RAY DIFFRACTION8(chain A and resid 338:433)A338 - 433
9X-RAY DIFFRACTION9(chain A and resid 434:456)A434 - 456
10X-RAY DIFFRACTION10(chain A and resid 457:496)A457 - 496
11X-RAY DIFFRACTION11(chain B and resid 1665:1671)B1665 - 1671
12X-RAY DIFFRACTION12(chain B and resid 1672:1676)B1672 - 1676
13X-RAY DIFFRACTION13(chain B and resid 1677:1686)B1677 - 1686

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