[English] 日本語
Yorodumi
- PDB-6q83: Crystal structure of the biportin Pdr6 in complex with UBC9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q83
TitleCrystal structure of the biportin Pdr6 in complex with UBC9
Components
  • Importin beta-like protein KAP122
  • UBC9
KeywordsPROTEIN TRANSPORT / Importin-Beta family / biportin / nuclear import / SUMOylation
Function / homology
Function and homology information


SUMO conjugating enzyme activity / mitotic spindle elongation / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of DNA damage response and repair proteins / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity ...SUMO conjugating enzyme activity / mitotic spindle elongation / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of DNA damage response and repair proteins / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear export / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / regulation of cell size / protein sumoylation / condensed nuclear chromosome / protein import into nucleus / nuclear envelope / cell division / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin beta-like protein KAP122 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.53 Å
AuthorsAksu, M. / Trakhanov, S. / Vera-Rodriguez, A. / Gorlich, D.
CitationJournal: J.Cell Biol. / Year: 2019
Title: Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.
Authors: Aksu, M. / Trakhanov, S. / Vera Rodriguez, A. / Gorlich, D.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 beta-like protein KAP122
B: UBC9


Theoretical massNumber of molelcules
Total (without water)141,3552
Polymers141,3552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint4 kcal/mol
Surface area53710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.260, 198.260, 289.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

-
Components

#1: Protein Importin beta-like protein KAP122 / Karyopherin-122 / Pleiotropic drug resistance regulatory protein 6


Mass: 123492.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: KAP122, PDR6, YGL016W / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 F' / References: UniProt: P32767
#2: Protein UBC9


Mass: 17862.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: P50623

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: Sodium cacodylate, magnesium chloride, ethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 4.53→49.565 Å / Num. obs: 12937 / % possible obs: 99.6 % / Redundancy: 10.072 % / Biso Wilson estimate: 226.685 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.178 / Χ2: 0.989 / Net I/σ(I): 11.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.53-4.659.2252.4920.928920.5782.63895.7
4.65-4.7810.4382.0991.189290.6382.207100
4.78-4.9110.7441.7531.449050.6241.841100
4.91-5.0610.7341.6381.518720.6471.72100
5.06-5.2310.6431.4231.768490.7181.495100
5.23-5.4110.581.3231.898090.7071.3999.9
5.41-5.6210.4541.2631.987860.8161.328100
5.62-5.8510.3711.1132.237660.811.171100
5.85-6.1110.1940.9052.827370.8470.953100
6.11-6.419.7250.7823.267100.8680.82699.9
6.41-6.758.9280.5254.826690.9580.558100
6.75-7.169.5890.3297.746370.9820.348100
7.16-7.6610.5670.19612.845960.9910.207100
7.66-8.2710.3770.11620.595620.9970.122100
8.27-9.0610.0290.0730.115170.9990.074100
9.06-10.139.6480.04244.254690.9990.044100
10.13-11.79.2130.03948.624270.9990.041100
11.7-14.338.1890.03650.113540.9990.038100
14.33-20.269.990.03159.332860.9990.033100
20.26-49.5659.1090.02860.661650.9990.0394.8

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJD and 6Q82

2gjd

6q82


Resolution: 4.53→49.565 Å / SU ML: 0.83 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.21
RfactorNum. reflection% reflection
Rfree0.2708 744 3.03 %
Rwork0.2593 --
obs0.2597 12912 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 351.26 Å2 / Biso mean: 311.3736 Å2 / Biso min: 289.44 Å2
Refinement stepCycle: final / Resolution: 4.53→49.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9380 0 0 0 9380
Num. residues----1168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.5301-4.87960.38461450.38864668481398
4.8796-5.37010.33521520.378347874939100
5.3701-6.14590.4451470.390747514898100
6.1459-7.73840.34491470.339147924939100
7.7384-49.56790.20631530.189847914944100

+
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