6Q82

Crystal structure of the biportin Pdr6 in complex with RanGTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.

Aksu, M.Trakhanov, S.Vera Rodriguez, A.Gorlich, D.

(2019) J.Cell Biol. 218: 1839-1852

  • DOI: 10.1083/jcb.201812093
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Importins ferry proteins into nuclei while exportins carry cargoes to the cytoplasm. In the accompanying paper in this issue (Vera Rodriguez et al. 2019. <i>J. Cell Biol. </i> https://doi.org/10.1083/jcb.201812091), we discovered that Pdr6 is a bipo ...

    Importins ferry proteins into nuclei while exportins carry cargoes to the cytoplasm. In the accompanying paper in this issue (Vera Rodriguez et al. 2019. J. Cell Biol. https://doi.org/10.1083/jcb.201812091), we discovered that Pdr6 is a biportin that imports, e.g., the SUMO E2 ligase Ubc9 while depleting the translation factor eIF5A from the nuclear compartment. In this paper, we report the structures of key transport intermediates, namely, of the Ubc9•Pdr6 import complex, of the RanGTP•Pdr6 heterodimer, and of the trimeric RanGTP•Pdr6•eIF5A export complex. These revealed nonlinear transport signals, chaperone-like interactions, and how the RanGTPase system drives Pdr6 to transport Ubc9 and eIF5A in opposite directions. The structures also provide unexpected insights into the evolution of transport selectivity. Specifically, they show that recognition of Ubc9 by Pdr6 differs fundamentally from that of the human Ubc9-importer Importin 13. Likewise, Pdr6 recognizes eIF5A in a nonhomologous manner compared with the mammalian eIF5A-exporter Exportin 4. This suggests that the import of Ubc9 and active nuclear exclusion of eIF5A evolved in different eukaryotic lineages more than once and independently from each other.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea. Electronic address: chahong@korea.ac.kr.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 106, Taiwan. andyhsu@ntu.edu.tw.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand.,Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands.,Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada.,Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA. Electronic address: qunliu@bnl.gov.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France.,SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. kwmiller@mgh.harvard.edu.,Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand emily.parker@vuw.ac.nz g.b.jameson@massey.ac.nz.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, Netherlands.,MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.,National Institute of Biological Sciences, Beijing, China.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 106, Taiwan.,Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institute , 5232 Villigen , Switzerland.,Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany goerlich@mpibpc.mpg.de.,Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nisimasu@bs.s.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA.,Dipartimento di Scienze della Terra , Università di Pisa , via Santa Maria 53 , 56126 Pisa , Italy.,Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea.,Laboratory Molecular and Cellular Signaling, Department Cellular and Molecular Medicine, Campus Gasthuisberg O/N-I Bus 802, Herestraat 49 3000 Leuven, Belgium.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica., Taipei, 115, Taiwan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. s.s.virdee@dundee.ac.uk.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan. bmchinp@ibms.sinica.edu.tw.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.,Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. simonasm@mrc-lmb.cam.ac.uk.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.,Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.,NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.,Institute of Neuropathology, University of Zurich, Switzerland.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA mr@purdue.edu.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Institute for Genetics, University of Cologne, Cologne, Germany.,Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.,Centro de Química Estrutural, Instituto Superior Técnico , Universidade de Lisboa , Av. Rovisco Pais 1 , 1049-001 Lisboa , Portugal.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette , France.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA. Electronic address: lei.shi2@nih.gov.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. radu@mrc-lmb.cam.ac.uk.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Department of Agricultural Chemistry, National Taiwan University, Taipei, 106, Taiwan. andyhsu@ntu.edu.tw.,McGovern Institute for Brain Research, Cambridge, MA 02139, USA.,Beijing Mingde Zhengkang Technologies Co., Ltd., Beijing, China.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA.,Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan.,Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA. Electronic address: mq2102@cumc.columbia.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Importin beta-like protein KAP122
A
1080Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: KAP122 (PDR6)
Find proteins for P32767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32767
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein Ran
B
176Homo sapiensMutation(s): 1 
Gene Names: RAN (ARA24)
Find proteins for P62826 (Homo sapiens)
Go to Gene View: RAN
Go to UniProtKB:  P62826
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.218 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 192.990α = 90.00
b = 192.990β = 90.00
c = 229.170γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
AutoSolphasing
PHENIXrefinement
RESOLVEmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references
  • Version 1.2: 2019-06-12
    Type: Data collection, Database references