[English] 日本語
Yorodumi
- PDB-6iua: Crystal structure of importin-alpha1 bound to the 53BP1 nuclear l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iua
TitleCrystal structure of importin-alpha1 bound to the 53BP1 nuclear localization signal (S1678D)
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


Sensing of DNA Double Strand Breaks / ubiquitin-modified histone reader activity / 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 ...Sensing of DNA Double Strand Breaks / ubiquitin-modified histone reader activity / 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 / 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 / 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: 1.7 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,7802
Polymers48,7802
Non-polymers00
Water8,557475
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint5 kcal/mol
Surface area19250 Å2
Unit cell
Length a, b, c (Å)79.260, 90.170, 97.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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: 2536.888 Da / Num. of mol.: 1 / Mutation: S1678D
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.: 475 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: sodium citrate, HEPES, DTT

-
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: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→24.53 Å / Num. obs: 77094 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 11 / Num. measured all: 493282 / Scaling rejects: 1325
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.736.60.99540450.7290.4161.08100
9-24.535.10.0515020.990.0240.05782.4

-
Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IU7

6iu7


Resolution: 1.7→24.324 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.16
RfactorNum. reflection% reflection
Rfree0.1786 3837 4.98 %
Rwork0.155 --
obs0.1562 77006 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.04 Å2 / Biso mean: 32.8333 Å2 / Biso min: 12.25 Å2
Refinement stepCycle: final / Resolution: 1.7→24.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 475 3872
Biso mean---44.06 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72150.2661410.266426882829100
1.7215-1.74420.27841470.256326732820100
1.7442-1.7680.28641480.246426842832100
1.768-1.79330.25911310.232226932824100
1.7933-1.82010.2551440.214226512795100
1.8201-1.84850.20141580.197926712829100
1.8485-1.87880.17611340.179927162850100
1.8788-1.91120.20961310.174326582789100
1.9112-1.94590.20761390.164227012840100
1.9459-1.98330.18851310.164527262857100
1.9833-2.02380.18481470.164126682815100
2.0238-2.06780.17911270.161526892816100
2.0678-2.11580.17161310.157427092840100
2.1158-2.16870.18121340.152926922826100
2.1687-2.22730.1771500.146126842834100
2.2273-2.29280.1731440.143526992843100
2.2928-2.36680.17351220.14427462868100
2.3668-2.45130.15591290.143227192848100
2.4513-2.54930.18251620.147426962858100
2.5493-2.66520.16141380.150327172855100
2.6652-2.80550.14181370.147627242861100
2.8055-2.9810.18121170.147527522869100
2.981-3.21070.16311370.152127512888100
3.2107-3.53290.1521970.149426892886100
3.5329-4.04210.16241600.125527632923100
4.0421-5.0850.16731550.133527792934100
5.085-24.32640.22591460.17762831297797
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)
13.00750.33250.16242.0106-0.07036.22590.18820.1401-0.1337-0.4078-0.05440.13920.2789-0.3674-0.04690.29980.0497-0.07490.19790.01670.2483-7.3682-62.10117.839
22.8491-0.24350.46832.5135-0.28183.61380.10390.2542-0.2485-0.4732-0.0556-0.23690.22120.3775-0.04250.28230.05060.00040.1947-0.01480.2308-3.3072-54.252510.7406
31.3886-0.14830.12911.6196-0.85592.51790.0256-0.085-0.14990.14880.04190.0190.00190.0365-0.11580.19850.0155-0.02560.14790.01180.1771-6.6453-47.86417.8306
40.98680.10280.13071.2466-0.09770.81380.061-0.05210.00020.08410.00370.00160.0706-0.0007-0.06310.1523-0.0054-0.00750.13740.00830.128-8.3499-36.076116.4727
51.91510.09160.08821.41940.4071.14060.04770.09380.01350.0752-0.0278-0.1460.12470.08030.00640.1642-0.022-0.00750.14130.00520.1798-0.089-28.155814.8192
69.5089-2.84695.82933.9679-1.64443.5805-0.1716-0.40860.43270.2520.15140.6332-0.6882-0.317-0.02240.21680.01570.04480.1969-0.00960.3184-10.9592-18.593814.8248
70.66560.599-0.35441.5632-1.011.81630.09260.00670.12950.1584-0.0580.0719-0.1030.0569-0.0430.1709-0.01710.01550.1736-0.00210.21793.6624-17.04638.0031
81.62060.3169-0.70861.3502-0.54341.31850.02890.250.1276-0.04140.01030.1087-0-0.1374-0.02390.11470.0074-0.00970.16670.0280.138911.2163-8.7882-11.1706
91.66450.7893-0.14636.11790.05371.68750.14340.68410.3733-0.3584-0.09560.5643-0.0118-0.5427-0.10060.33370.0655-0.10470.51290.14950.29284.7133-3.0197-24.1737
102.3360.3632-0.17592.9855-0.00911.6732-0.05260.86910.0498-1.1920.00510.31140.0114-0.66330.03470.7379-0.0039-0.15490.90650.07280.31595.6474-6.183-33.3958
113.83191.7193-1.13715.86661.67734.67240.08020.45590.0911-0.36880.0160.37970.4383-0.2909-0.08410.2403-0.0265-0.04430.28660.05220.2704-2.415-14.7611-7.7672
121.8053-2.07591.60733.1177-3.86597.0032-0.04950.5032-0.1208-0.6859-0.1861-0.01040.01140.11780.09390.9394-0.01920.1760.7130.09620.90360.5106-31.745-5.1775
134.012-0.9972.90973.6557-2.33656.00980.21410.2379-0.3015-0.27940.0042-0.4082-0.07520.3377-0.1390.18870.0290.01590.28340.0310.25743.049-41.02329.9273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 76:92)A76 - 92
2X-RAY DIFFRACTION2(chain A and resid 93:122)A93 - 122
3X-RAY DIFFRACTION3(chain A and resid 123:153)A123 - 153
4X-RAY DIFFRACTION4(chain A and resid 154:214)A154 - 214
5X-RAY DIFFRACTION5(chain A and resid 215:245)A215 - 245
6X-RAY DIFFRACTION6(chain A and resid 246:251)A246 - 251
7X-RAY DIFFRACTION7(chain A and resid 252:329)A252 - 329
8X-RAY DIFFRACTION8(chain A and resid 330:432)A330 - 432
9X-RAY DIFFRACTION9(chain A and resid 433:457)A433 - 457
10X-RAY DIFFRACTION10(chain A and resid 458:496)A458 - 496
11X-RAY DIFFRACTION11(chain B and resid 1665:1672)B1665 - 1672
12X-RAY DIFFRACTION12(chain B and resid 1673:1679)B1673 - 1679
13X-RAY DIFFRACTION13(chain B and resid 1680:1686)B1680 - 1686

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more