6TB3

yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

The Ccr4-Not complex monitors the translating ribosome for codon optimality.

Buschauer, R.Matsuo, Y.Sugiyama, T.Chen, Y.H.Alhusaini, N.Sweet, T.Ikeuchi, K.Cheng, J.Matsuki, Y.Nobuta, R.Gilmozzi, A.Berninghausen, O.Tesina, P.Becker, T.Coller, J.Inada, T.Beckmann, R.

(2020) Science 368

  • DOI: 10.1126/science.aay6912
  • Primary Citation of Related Structures:  
    6TB3, 6TNU

  • PubMed Abstract: 
  • Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality ...

    Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de toshifumi.inada.a3@tohoku.ac.jp jmc71@case.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AC [auth P]206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 4
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40S ribosomal protein S1-AD [auth Q]232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 5
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40S ribosomal protein S15E117Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2F [auth R]216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 7
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40S ribosomal protein S3G [auth A]222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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40S ribosomal protein S4-AH [auth S]258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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40S ribosomal protein S5I [auth B]206Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S6-AJ [auth T]228Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 11
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40S ribosomal protein S7-AK [auth U]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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40S ribosomal protein S8L [auth V]187Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
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40S ribosomal protein S9-AM [auth W]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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40S ribosomal protein S10-AN [auth C]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 15
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40S ribosomal protein S11-AO [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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40S ribosomal protein S12P [auth D]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 17
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40S ribosomal protein S13Q [auth Y]150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 18
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40S ribosomal protein S14-BR [auth Z]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14BCRY2YJL191WJ0354
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Entity ID: 19
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40S ribosomal protein S16-AS [auth F]141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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40S ribosomal protein S17-BT [auth G]125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17BRP51BYDR447C
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40S ribosomal protein S18-AU [auth H]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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40S ribosomal protein S19-AV [auth I]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 23
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40S ribosomal protein S20W [auth J]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 25
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40S ribosomal protein S21-AY [auth a]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AZ [auth b]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 27
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40S ribosomal protein S23-AAA [auth c]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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40S ribosomal protein S24-ABA [auth d]134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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40S ribosomal protein S25-ACA [auth K]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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40S ribosomal protein S26-BDA [auth e]97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
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40S ribosomal protein S27-AEA [auth f]81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 32
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40S ribosomal protein S29-AFA [auth M]53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 33
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40S ribosomal protein S30-AGA [auth g]60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Ubiquitin-40S ribosomal protein S31HA [auth N]73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Guanine nucleotide-binding protein subunit beta-like proteinIA [auth O]312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 36
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40S ribosomal protein S28-AJA [auth L]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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60S ribosomal protein L1-ALA [auth BT]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL1ASSM1SSM1AYPL220W
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Entity ID: 41
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60S ribosomal protein L2-AOA [auth AW]251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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60S ribosomal protein L3PA [auth BA]386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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60S ribosomal protein L4-AQA [auth BE]361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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60S ribosomal protein L5RA [auth BI]294Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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60S ribosomal protein L6-BSA [auth BM]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6BRPL16BRPL17BYL16BYLR448WL9324.4
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60S ribosomal protein L7-ATA [auth BO]222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 47
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60S ribosomal protein L8-AUA [auth AA]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 48
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60S ribosomal protein L9-AVA [auth AD]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 49
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60S ribosomal protein L10WA [auth BD]218Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 50
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60S ribosomal protein L11-BXA [auth AG]169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 51
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60S ribosomal protein L13-AYA [auth AJ]193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 52
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60S ribosomal protein L14-AZA [auth AM]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 53
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60S ribosomal protein L15-AAB [auth AQ]203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 54
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60S ribosomal protein L16-ABB [auth AU]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 55
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60S ribosomal protein L17-ACB [auth AX]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 56
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60S ribosomal protein L18-ADB [auth BB]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 57
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60S ribosomal protein L19-AEB [auth BF]188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 58
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60S ribosomal protein L20-AFB [auth BH]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 59
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60S ribosomal protein L21-AGB [auth BJ]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 60
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60S ribosomal protein L22-AHB [auth BL]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 61
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60S ribosomal protein L23-AIB [auth AB]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 62
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60S ribosomal protein L24-AJB [auth AE]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 63
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60S ribosomal protein L25KB [auth AH]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 64
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60S ribosomal protein L26-ALB [auth AK]125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 65
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60S ribosomal protein L27-AMB [auth AN]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 66
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60S ribosomal protein L28NB [auth AR]148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 67
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60S ribosomal protein L29OB [auth AV]58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 68
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60S ribosomal protein L30PB [auth AY]96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 69
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60S ribosomal protein L31-AQB [auth BC]109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 70
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60S ribosomal protein L32RB [auth BG]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 71
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60S ribosomal protein L33-ASB [auth BK]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 72
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60S ribosomal protein L34-ATB [auth BN]112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 73
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60S ribosomal protein L35-AUB [auth BP]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 74
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60S ribosomal protein L36-AVB [auth AC]99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 75
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60S ribosomal protein L37-AWB [auth AF]81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 76
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60S ribosomal protein L38XB [auth AI]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 77
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60S ribosomal protein L39YB [auth AL]50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 78
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Ubiquitin-60S ribosomal protein L40ZB [auth AO]52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 79
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60S ribosomal protein L41-BAC [auth AS]25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41BRPL47BYL41BYDL133C-AYDL133BC
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Entity ID: 80
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60S ribosomal protein L42-ABC [auth AP]103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 81
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60S ribosomal protein L43-ACC [auth AT]91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 82
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60S ribosomal protein L41-ADC [auth BV]22Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 83
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General negative regulator of transcription subunit 5EC [auth BW]112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOT5YPR072WYP9499.27
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Entity ID: 1
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Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNAA [auth 2]1798Saccharomyces cerevisiae S288C
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Entity ID: 2
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mRNAB [auth l]3Saccharomyces cerevisiae S288C
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Entity ID: 24
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tRNAX [auth n]75Saccharomyces cerevisiae S288C
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Entity ID: 37
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25S rRNAKA [auth BQ]3223Saccharomyces cerevisiae S288C
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Entity ID: 39
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5S rRNAMA [auth BR]121Saccharomyces cerevisiae S288C
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Entity ID: 40
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5.8S rRNANA [auth BS]158Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

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JO [auth BQ]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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AP,
BP [auth AT],
VF [auth M],
WF [auth N],
WO [auth BN],
AP,
BP [auth AT],
VF [auth M],
WF [auth N],
WO [auth BN],
YO [auth AF],
ZO [auth AO]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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