6I7O

The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.3 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

Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways.

Ikeuchi, K.Tesina, P.Matsuo, Y.Sugiyama, T.Cheng, J.Saeki, Y.Tanaka, K.Becker, T.Beckmann, R.Inada, T.

(2019) EMBO J. 38: --

  • DOI: 10.15252/embj.2018100276

  • PubMed Abstract: 
  • Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we r ...

    Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGD RQC + ) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGD RQC - ) can occur in a Not4-dependent manner.


    Organizational Affiliation

    Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia. Electronic address: r.mcgeary@uq.edu.au.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K. jworrall@essex.ac.uk.,State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Drug Discovery Group Cancer Research UK Manchester Institute, Manchester, UK.,Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,the Departments of Life Sciences and.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K. c.dong@uea.ac.uk.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,D. E. Shaw Research, New York, NY, USA.,Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China.,Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Structural Biology Research Center, VIB, Brussels, Belgium.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.,the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and.,Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan.,Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Shanghai Institute of Precision Medicine, Shanghai 200125, China.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan. jysuh@snu.ac.kr.,Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wfeng@ibp.ac.cn.,Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, 02792, Korea.,Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA.,the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Electronic address: ckerfeld@lbl.gov.,Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia; Helwan University, Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan, Egypt.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. jysuh@snu.ac.kr.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria, christian.obinger@boku.ac.at.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Medicinal Chemistry, Department of Internal Medicine, Comprehensive Cancer Center, and Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland. Electronic address: mbretner@ch.pw.edu.pl.,Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. chengzh@pitt.edu.,Dropbox, New York, NY, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Bioss Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia.,Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.,Department of Biochemistry & Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, wipa@sut.ac.th.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA williamsrs@niehs.nih.gov.,Biomedical Sciences, Defence Science and Technology Laboratory Porton Down, SP4 0JQ Salisbury, United Kingdom.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.,the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium.,Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
AW, XW
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
BA, YA
386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL3
Go to UniProtKB:  P14126
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
BE, YE
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10664
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
BI, YI
294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL5
Go to UniProtKB:  P26321
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
BM, YM
176Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
BO, YO
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
AA, XA
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
AD, XD
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
BD, YD
221Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL10
Go to UniProtKB:  P41805
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
AG, XG
169Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11B (RP39B, RPL16B)
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E757
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
AJ, XJ
194Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL13A
Go to UniProtKB:  Q12690
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
AM, XM
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36105
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
AQ, XQ
203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
AU, XU
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
P, Pb
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
Q, Qb
216Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33442
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
R, Rb
217Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS2
Go to UniProtKB:  P25443
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
A, Ab
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS3
Go to UniProtKB:  P05750
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
S, Sb
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
B, Bb
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P26783
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
T, Tb
218Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
U, Ub
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
V, Vb
200Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
W, Wb
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
C, Cb
92Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08745
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
X, Xb
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
D, Db
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
Y, Yb
150Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-B
Z, Zb
128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS14B (CRY2)
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39516
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
E, Eb
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS15
Go to UniProtKB:  Q01855
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
F, Fb
141Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-A
G, Gb
125Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS17A (RP51A)
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02407
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
H, Hb
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
I, Ib
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS19A (RP55A, RPS16AA)
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07280
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
J, Jb
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS20
Go to UniProtKB:  P38701
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
a, ab
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0V8
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
b, bb
129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
c, cb
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX29
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
d, db
134Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
K, Kb
69Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E792
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-B
e, eb
97Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS26B
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39939
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
f, fb
81Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS27A
Go to UniProtKB:  P35997
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
L, Lb
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
M, Mb
53Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS29A (RPS36A, YS29A)
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41057
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
g, gb
60Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
N, Nb
73Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
O, Ob
313Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38011
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
AX, XX
184Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
BB, YB
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
Go to UniProtKB:  P0CX49
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
BF, YF
188Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX82
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
BH, YH
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX23
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
BJ, YJ
159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
BL, YL
98Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05749
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
AB, XB
134Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
AE, XE
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
AH, XH
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
AK, XK
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05743
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
AN, XN
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL27A
Go to UniProtKB:  P0C2H6
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
AR, XR
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
Go to UniProtKB:  P02406
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
AV, XV
58Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL29
Go to UniProtKB:  P05747
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
AY, XY
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL30
Go to UniProtKB:  P14120
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
BC, YC
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
BG, YG
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL32
Go to UniProtKB:  P38061
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
BK, YK
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
BN, YN
112Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P87262
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
BP, YP
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
AC, XC
99Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
AF, XF
82Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
AI, XI
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
AL, XL
50Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
AO, XO
52Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-B
AS, XS
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL41B (RPL47B, YL41B)
Find proteins for P0CX87 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX87
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
AP, XP
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
AT, XT
91Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX25
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
BU, YU
312Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPP0 (L10E, RPA0, RPL10E, RPLA0)
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05317
Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNABQ,YQ3396Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNABR,YR121Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNABS,YS157Saccharomyces cerevisiae
Entity ID: 18
MoleculeChainsLengthOrganism
18S ribosomal RNA2,2b1800Saccharomyces cerevisiae
Entity ID: 80
MoleculeChainsLengthOrganism
P-site tRNAn76Saccharomyces cerevisiae
Entity ID: 81
MoleculeChainsLengthOrganism
E-site tRNAm75Saccharomyces cerevisiae
Entity ID: 82
MoleculeChainsLengthOrganism
A/P hybrid tRNAnb76Saccharomyces cerevisiae
Entity ID: 83
MoleculeChainsLengthOrganism
P/E hybrid tRNAmb77Saccharomyces cerevisiae
Entity ID: 84
MoleculeChainsLengthOrganism
mRNAl57Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AO, AP, AT, e, eb, f, fb, M, Mb, N, XF, XO, XP, XT, YN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanyBE1814/15-1
Japan Society for the Promotion of ScienceJapan26116003

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references