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- PDB-8hkw: Crystal structure of importin-alpha3 bound to the 53BP1 nuclear l... -

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Basic information

Entry
Database: PDB / ID: 8hkw
TitleCrystal structure of importin-alpha3 bound to the 53BP1 nuclear localization signal
Components
  • Importin subunit alpha-3
  • Peptide from TP53-binding protein 1
KeywordsTRANSPORT PROTEIN / importin alpha / nuclear localization signal / nuclear import
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / dopamine secretion / positive regulation of isotype switching / cellular response to X-ray / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / 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 ...ubiquitin-modified histone reader activity / dopamine secretion / positive regulation of isotype switching / cellular response to X-ray / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / 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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / nuclear pore / methylated histone binding / histone reader activity / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / positive regulation of DNA-binding transcription factor activity / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / ISG15 antiviral mechanism / double-strand break repair via nonhomologous end joining / protein import into nucleus / p53 binding / 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 / gene expression / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
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 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Armadillo-like helical / Armadillo-type fold / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
Importin subunit alpha-3 / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatsuura, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06104 Japan
CitationJournal: Data Brief / Year: 2023
Title: Crystallographic data of an importin-alpha 3 dimer in which the two protomers are bridged by a bipartite nuclear localization signal.
Authors: Matsuura, Y.
History
DepositionNov 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-3
B: Importin subunit alpha-3
C: Peptide from TP53-binding protein 1
D: Peptide from TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)96,5404
Polymers96,5404
Non-polymers00
Water9,044502
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.703, 79.600, 117.440
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Importin subunit alpha-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 45761.113 Da / Num. of mol.: 2 / Fragment: UNP residues 70-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00629
#2: Protein/peptide Peptide from TP53-binding protein 1 / p53BP1


Mass: 2508.878 Da / Num. of mol.: 2
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.: 502 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Mother liquor contained PEG3350 and lithium nitrate. Crystal was grown in the presence of a synthetic peptide (amino acid sequence: GTSFSGRKIKTAVRRRK) that corresponds to human Nup153 residues 1459-1475).

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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: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→27.34 Å / Num. obs: 68772 / % possible obs: 99.4 % / Redundancy: 3 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.993 / Net I/σ(I): 4.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4433 / CC1/2: 0.338 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXv1.14refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.338 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 3548 5.17 %
Rwork0.2006 --
obs0.2017 68669 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 0 502 7252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036892
X-RAY DIFFRACTIONf_angle_d0.5359402
X-RAY DIFFRACTIONf_dihedral_angle_d14.3254222
X-RAY DIFFRACTIONf_chiral_restr0.0381128
X-RAY DIFFRACTIONf_plane_restr0.0041224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9260.40371420.37872561X-RAY DIFFRACTION98
1.926-1.95350.38111250.362613X-RAY DIFFRACTION99
1.9535-1.98270.38061490.34612548X-RAY DIFFRACTION99
1.9827-2.01370.36761400.31232626X-RAY DIFFRACTION99
2.0137-2.04670.30241400.2972568X-RAY DIFFRACTION99
2.0467-2.08190.30721540.27272610X-RAY DIFFRACTION99
2.0819-2.11980.33471480.26392595X-RAY DIFFRACTION100
2.1198-2.16050.30071490.2582593X-RAY DIFFRACTION99
2.1605-2.20460.28251270.2382597X-RAY DIFFRACTION99
2.2046-2.25250.25661390.24022562X-RAY DIFFRACTION99
2.2525-2.30490.23891440.22082587X-RAY DIFFRACTION98
2.3049-2.36250.26981510.22542571X-RAY DIFFRACTION98
2.3625-2.42640.2121430.2052565X-RAY DIFFRACTION99
2.4264-2.49770.23781600.20712641X-RAY DIFFRACTION100
2.4977-2.57830.26981410.20872606X-RAY DIFFRACTION100
2.5783-2.67030.24241280.21582623X-RAY DIFFRACTION100
2.6703-2.77720.23221360.20732618X-RAY DIFFRACTION100
2.7772-2.90340.24791370.212631X-RAY DIFFRACTION100
2.9034-3.05630.23441380.20662632X-RAY DIFFRACTION100
3.0563-3.24750.21271450.20152569X-RAY DIFFRACTION99
3.2475-3.49780.2341470.21082575X-RAY DIFFRACTION98
3.4978-3.84890.17751350.17032644X-RAY DIFFRACTION100
3.8489-4.40390.16151410.15322650X-RAY DIFFRACTION100
4.4039-5.54080.17751490.16342660X-RAY DIFFRACTION100
5.5408-27.3380.16371400.15892676X-RAY DIFFRACTION99
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)
10.0787-0.0589-0.1140.09270.12410.1521-0.2360.50590.279-0.84510.10850.3634-0.15460.0751-0.00010.4608-0.0138-0.04560.31670.05750.335920.0201-67.2669-48.9644
20.2265-0.005-0.1020.1378-0.10890.1613-0.0619-0.03090.27090.2351-0.12-0.10520.10720.1595-00.3384-0.0297-0.10180.32560.01150.446616.4214-61.681-36.9599
31.8423-0.6222-0.10240.99280.04910.9580.01850.02610.0532-0.0848-0.0626-0.03080.05370.039800.2609-0.028-0.00040.22570.03570.27364.983-57.9965-43.0969
40.5074-0.2090.11630.1054-0.00070.466-0.0266-0.0429-0.05010.0126-0.00330.0247-0.0584-0.0624-00.2861-0.03140.00080.25790.04030.3215-7.6134-54.9973-34.3898
50.1138-0.1449-0.04890.16620.02810.2462-0.06640.1440.4105-0.3925-0.19310.897-0.1836-0.4975-0.00040.3622-0.0398-0.02450.3154-0.03540.4071-13.4146-43.0383-37.793
60.42070.3125-0.5321.14970.92261.1713-0.0450.047-0.14470.0173-0.0350.029-0.023-0.046-00.2052-0.0223-0.01580.24010.0110.2227-15.3938-43.2827-20.4986
70.04650.0537-0.00750.0218-0.03090.0187-0.5888-0.1927-0.4114-0.34930.2362-0.4760.30580.75590.00010.35660.05360.00560.4528-0.00080.4055-4.4172-36.7408-8.962
80.32450.07140.8120.5926-0.08820.8072-0.073-0.24190.02810.00660.0284-0.0187-0.2454-0.1034-00.2945-0.0063-0.00570.345-0.00450.256-15.4477-24.7072-8.8882
90.27220.0950.13950.5185-0.16140.2299-0.44210.03770.54080.0220.0569-0.3179-0.52660.106-00.4923-0.0377-0.1640.318-0.0040.4491-7.6559-14.2713-9.8774
101.6181-0.31760.27660.62110.25240.5085-0.06321.79932.1834-0.1911-0.8557-0.6424-1.6362-0.10710.0131.059-0.3044-0.5781-0.274-0.48150.6136-7.9528-4.9673-8.7834
110.44050.1113-0.08290.1287-0.05370.1675-0.1993-0.15040.1224-0.2109-0.1382-0.05880.01250.0041-0.00080.27620.03620.02390.3432-0.01470.389-12.3862-7.8727-43.8403
120.9474-1.0017-0.0121.16060.61060.6771-0.0514-0.0421-0.0283-0.1511-0.03530.0829-0.0726-0.1427-00.2919-0.0191-0.00320.28240.00660.2921-4.815-13.1977-43.2795
131.0828-0.77450.09660.8184-0.2250.9493-0.05040.0395-0.1158-0.09290.06950.02630.0332-0.056400.2395-0.01190.00420.2028-0.0080.26957.4245-18.6483-41.8407
140.62840.0794-0.64410.4407-0.11540.6588-0.1898-0.23540.0453-0.22620.11630.17630.02770.1463-00.2640.017-0.02090.2318-0.02210.301913.6964-21.9587-32.4165
150.09120.10090.22440.5834-0.33270.3869-0.05540.02510.03720.17970.033-0.10370.04990.043400.28750.0161-0.02380.31930.00690.371818.2621-23.1832-25.68
161.15070.05530.77812.0381-0.41950.8877-0.0789-0.17460.11540.10160.009-0.0047-0.0443-0.1221-0.00010.27090.03510.04120.3374-0.03880.222621.2779-36.115-17.0041
170.2307-0.344-0.26331.3513-0.17070.4412-0.0964-0.2592-0.18030.4880.16690.25410.1835-0.24310.02940.3544-0.01820.10230.40880.05720.260817.4722-51.7615-6.9253
180.11760.0609-0.04240.12850.08460.05340.0940.3161-0.3204-0.2484-0.05040.20950.5807-0.18220.00020.5082-0.0550.05840.46560.14050.532917.9115-61.8832-12.1944
190.0898-0.0528-0.18090.69740.18820.2474-0.116-0.5182-1.22750.12790.05690.77920.7594-0.28060.00020.8823-0.18390.16410.70780.2640.980411.3144-67.5006-8.1409
200.0155-0.00260.00930.01070.0064-0.00280.11630.4022-0.1742-0.03720.1027-0.03120.70480.183700.9981-0.09790.06890.54930.00421.007815.585-72.3106-11.7008
210.30040.09690.1260.0563-0.00060.07030.1898-0.0701-0.39960.24790.2655-0.3383-0.32240.46350.00860.3768-0.05330.11880.3765-0.02510.2856-11.2004-27.7994-22.341
220.03160.01270.00510.03220.00240.00350.0702-0.062-0.26350.17490.04260.51880.24040.149-0.00010.7461-0.13310.07160.9320.09280.68781.3662-30.636-23.6239
230.02940.12810.05190.12520.02520.01360.0329-0.2786-0.57980.16390.14480.2135-0.1116-0.1999-00.38240.04270.02180.43440.05030.37790.5333-20.8435-29.2926
240.0930.03560.01230.03660.04870.03260.0646-0.17220.64920.12750.29960.73740.4458-0.49970.00120.3464-0.0447-0.06760.37720.03090.463316.8505-45.7863-22.353
250.00830.0111-0.00390.03430.00550.01040.04590.09620.10440.4610.3583-0.6017-0.01030.4677-0.00030.5975-0.0948-0.00370.74880.03560.95292.9418-43.6871-23.7853
260.05930.0343-0.01270.04630.02990.02360.00930.04130.35920.3591-0.1218-0.5020.30050.4726-0.00020.48030.0089-0.02660.3413-0.00690.34197.0531-54.8042-30.8588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 71:87)
2X-RAY DIFFRACTION2(chain A and resid 88:105)
3X-RAY DIFFRACTION3(chain A and resid 106:192)
4X-RAY DIFFRACTION4(chain A and resid 193:230)
5X-RAY DIFFRACTION5(chain A and resid 231:243)
6X-RAY DIFFRACTION6(chain A and resid 244:334)
7X-RAY DIFFRACTION7(chain A and resid 335:345)
8X-RAY DIFFRACTION8(chain A and resid 346:410)
9X-RAY DIFFRACTION9(chain A and resid 411:441)
10X-RAY DIFFRACTION10(chain A and resid 442:485)
11X-RAY DIFFRACTION11(chain B and resid 71:102)
12X-RAY DIFFRACTION12(chain B and resid 103:144)
13X-RAY DIFFRACTION13(chain B and resid 145:207)
14X-RAY DIFFRACTION14(chain B and resid 208:239)
15X-RAY DIFFRACTION15(chain B and resid 240:269)
16X-RAY DIFFRACTION16(chain B and resid 270:360)
17X-RAY DIFFRACTION17(chain B and resid 361:425)
18X-RAY DIFFRACTION18(chain B and resid 426:443)
19X-RAY DIFFRACTION19(chain B and resid 444:475)
20X-RAY DIFFRACTION20(chain B and resid 476:485)
21X-RAY DIFFRACTION21(chain C and resid 1666:1670)
22X-RAY DIFFRACTION22(chain C and resid 1671:1676)
23X-RAY DIFFRACTION23(chain C and resid 1677:1686)
24X-RAY DIFFRACTION24(chain D and resid 1666:1670)
25X-RAY DIFFRACTION25(chain D and resid 1671:1678)
26X-RAY DIFFRACTION26(chain D and resid 1679:1686)

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