6D6Q

Human nuclear exosome-MTR4 RNA complex - overall reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.

Weick, E.M.Puno, M.R.Januszyk, K.Zinder, J.C.DiMattia, M.A.Lima, C.D.

(2018) Cell 173: 1663

  • DOI: 10.1016/j.cell.2018.05.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Sch ...

    The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.


    Organizational Affiliation

    Graduate School of Science and Molecular Chirality Research Center, Chiba University, Inage, Chiba, Japan.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA. Electronic address: amy.howell@uconn.edu.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA. Electronic address: limac@mskcc.org.,Medicinal Chemistry & Drug Discovery, Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , U.K.,From the State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China and.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan. narita.akihiro@f.mbox.nagoya-u.ac.jp.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Cellular and Molecular Medicine, School of Medicine, and Section of Molecular Biology, Division of Biological Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.,Biogen Inc, Cambridge, MA.,Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan.,Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto, 610-0394, Japan.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA. Electronic address: marzena.pazgier@usuhs.edu.,Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, SP, Brazil.,Centre for Biological Sciences, B85 Life Sciences Building M55, University of Southampton, Southampton SO17 1BJ, UK. Electronic address: j.m.werner@soton.ac.uk.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: steven.porcelli@einstein.yu.edu.,Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.,Saverna Therapeutics AG , Pumpmattenweg 3 , CH-4105 Biel-Benken , Switzerland.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, 92093.,Biochemistry, Faculty of Chemistry, University of Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663, Kaiserslautern, Germany.,Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi, 480-1192, Japan.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany. ulrich.ermler@biophys.mpg.de.,Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. Electronic address: mario.murakami@ctbe.cnpem.br.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,From the State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China and chenlijuan125@163.com.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China. Electronic address: zhaole2@mail.xjtu.edu.cn.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK . Email: mahough@essex.ac.uk.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,PhD Program in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal.,Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany.,Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea.,Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. adha@ufl.edu.,Sprint Bioscience AB , Hälsovägen 7 , SE-141 57 Huddinge , Sweden.,CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.,From the High Pressure and Synchrotron Radiation Physics Division and ravimakde@rrcat.gov.in.,Institute for Interdisciplinary Research (IIIC), University of Coimbra, 3030-789 Coimbra, Portugal.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Centre for Biological Sciences, B85 Life Sciences Building M55, University of Southampton, Southampton SO17 1BJ, UK.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. r.suno@mfour.med.kyoto-u.ac.jp.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany. U.Rau@tu-bs.de.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging at the University of Melbourne, Melbourne, Australia.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. koss@bsd.uchicago.edu.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal; ppereira@ibmc.up.pt numenius@cnc.uc.pt.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany. matthias.boll@biologie.uni-freiburg.de.,Key Laboratory of Fermentation Engineering, Ministry of Education, College of Bioengineering, Hubei University of Technology, Wuhan, China; Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,AstraZeneca R&D, Darwin Building Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Korea.,Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel; The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan 52900, Israel. Electronic address: yanay@ofranlab.org.,Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.,Biochemistry Department, Indian Institute of Science, Bangalore 560012, India.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States.,Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India and snjam@barc.gov.in.,Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. yok5@snu.ac.kr.,Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany. Electronic address: raimund.wagener@uni-koeln.de.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Millennium Institute on Immunology and Immunotherapy, Programa de Inmunologia, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Korea.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Computational Biochemistry, University of Bayreuth, Universitätsstrasse 30, NW I, 95447, Bayreuth, Germany.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,RIKEN, SPring-8 Center, Hyogo, Japan.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil; Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,University of Chinese Academy of Sciences, Beijing, China.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,Bioverativ, a Sanofi company, Waltham, MA; and.,From the High Pressure and Synchrotron Radiation Physics Division and.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.,School of Biochemistry, Devi Ahilya University, Indore 452001, India.,Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA.,Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK. s.helaine@imperial.ac.uk.,Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA.,Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA . Email: candrew@eou.edu.,School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA. bruner@chem.ufl.edu.,National Institute for Research in Tuberculosis, Chennai 600031, India.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. ss1@nih.gov.,Biophysics, Department of Physics, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany.,Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA.,Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. eric.xu@vai.org.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. ss1@nih.gov.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, United States.,Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Faculty of Health and Welfare, Tokai Gakuin University, Nakakirino-cyo 5-68, Kakamigahara, Gifu, 504-8511, Japan.,Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Children's Hospital Boston, Boston, MA.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK.,Biochemistry Department, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,College of Medicine, Department of Biochemistry and Molecular Biology , University of Florida , Gainesville , Florida 32610 , United States.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia. Electronic address: jerome.lenours@monash.edu.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. koss@bsd.uchicago.edu.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA. eric.xu@vai.org.,Department of Chemistry, University of California, San Diego, La Jolla, California, 92093.,Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal; ppereira@ibmc.up.pt numenius@cnc.uc.pt.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France.,Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, 92093.,Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. Electronic address: priscila.giuseppe@ctbe.cnpem.br.,the Guangdong Zhongsheng Pharmaceutical Co., Ltd., Dongguan, Guangdong 523325, China.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Protech Inc., Yongeon 103 Daehangno, Jongno-gu, Seoul, 110-799, Republic of Korea. yok5@snu.ac.kr.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: mrn@iisc.ac.in.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 728 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6085, USA.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A
473Homo sapiensMutation(s): 0 
Gene Names: EXOSC9 (PMSCL1)
Find proteins for Q06265 (Homo sapiens)
Go to Gene View: EXOSC9
Go to UniProtKB:  Q06265
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP41
B
249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4 (RRP41, SKI6)
Find proteins for Q9NPD3 (Homo sapiens)
Go to Gene View: EXOSC4
Go to UniProtKB:  Q9NPD3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C
278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8 (OIP2, RRP43)
Find proteins for Q96B26 (Homo sapiens)
Go to Gene View: EXOSC8
Go to UniProtKB:  Q96B26
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D
237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5 (CML28, RRP46)
Find proteins for Q9NQT4 (Homo sapiens)
Go to Gene View: EXOSC5
Go to UniProtKB:  Q9NQT4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E
293Homo sapiensMutation(s): 0 
Gene Names: EXOSC7 (KIAA0116, RRP42)
Find proteins for Q15024 (Homo sapiens)
Go to Gene View: EXOSC7
Go to UniProtKB:  Q15024
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F
272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6 (MTR3)
Find proteins for Q5RKV6 (Homo sapiens)
Go to Gene View: EXOSC6
Go to UniProtKB:  Q5RKV6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G
277Homo sapiensMutation(s): 0 
Gene Names: EXOSC3 (RRP40)
Find proteins for Q9NQT5 (Homo sapiens)
Go to Gene View: EXOSC3
Go to UniProtKB:  Q9NQT5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H
296Homo sapiensMutation(s): 0 
Gene Names: EXOSC2 (RRP4)
Find proteins for Q13868 (Homo sapiens)
Go to Gene View: EXOSC2
Go to UniProtKB:  Q13868
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
I
197Homo sapiensMutation(s): 0 
Gene Names: EXOSC1 (CSL4)
Find proteins for Q9Y3B2 (Homo sapiens)
Go to Gene View: EXOSC1
Go to UniProtKB:  Q9Y3B2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome component 10
J
761Homo sapiensMutation(s): 1 
Gene Names: EXOSC10 (PMSCL, PMSCL2, RRP6)
EC: 3.1.13.-
Find proteins for Q01780 (Homo sapiens)
Go to Gene View: EXOSC10
Go to UniProtKB:  Q01780
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP44
K
960Homo sapiensMutation(s): 2 
Gene Names: DIS3 (KIAA1008, RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q9Y2L1 (Homo sapiens)
Go to Gene View: DIS3
Go to UniProtKB:  Q9Y2L1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 6
L
162Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH6 (MPP6)
Find proteins for Q99547 (Homo sapiens)
Go to Gene View: MPHOSPH6
Go to UniProtKB:  Q99547
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Exosome RNA helicase MTR4
M
1045Homo sapiensMutation(s): 0 
Gene Names: MTREX (DOB1, KIAA0052, MTR4, SKIV2L2)
EC: 3.6.4.13
Find proteins for P42285 (Homo sapiens)
Go to UniProtKB:  P42285
Entity ID: 14
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')N16synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA/RNA (62-MER)O62synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
M
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118080
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references