7NRD

Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of Gcn1 bound to stalled and colliding 80S ribosomes.

Pochopien, A.A.Beckert, B.Kasvandik, S.Berninghausen, O.Beckmann, R.Tenson, T.Wilson, D.N.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2022756118
  • Primary Citation of Related Structures:  
    7NRC, 7NRD

  • PubMed Abstract: 
  • The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for the kinase Gcn2, which in turn is activated by stalled ribosomes, leading to phosphorylation of eIF2 and a subsequent global repression of translation ...

    The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for the kinase Gcn2, which in turn is activated by stalled ribosomes, leading to phosphorylation of eIF2 and a subsequent global repression of translation. The fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, a negative regulator of Gcn2. Despite the wealth of available biochemical data, information on structures of Gcn proteins on the ribosome has remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the P-stalk and the A-site region of the lead ribosome. The lead ribosome is stalled in a nonrotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, and Rbg2/Gir2 in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site, and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings reveal the interaction mode of the Gcn2-activating protein Gcn1 with colliding ribosomes and provide insight into the regulation of Gcn2 activation. The binding of Gcn1 to a disome has important implications not only for the Gcn2-activated ISR, but also for the general ribosome-associated quality control pathways.


    Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; daniel.wilson@chemie.uni-hamburg.de.



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40S ribosomal protein S3B [auth SA]223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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40S ribosomal protein S5C [auth SB]206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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40S ribosomal protein S10-AD [auth SC]92Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S12E [auth SD]124Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S15F [auth SE]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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40S ribosomal protein S16-AG [auth SF]141Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S17-BH [auth SG]125Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S18-AI [auth SH]145Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S19-AJ [auth SI]143Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S20K [auth SJ]101Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S25-AL [auth SK]69Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S28-AM [auth SL]63Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S29-AN [auth SM]53Saccharomyces cerevisiae S288CMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31O [auth SN]73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Guanine nucleotide-binding protein subunit beta-like proteinP [auth SO]313Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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40S ribosomal protein S0-AQ [auth SP]206Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S1-AR [auth SQ]216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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40S ribosomal protein S2S [auth SR]217Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S4-AT [auth SS]260Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S6-AU [auth ST]218Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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40S ribosomal protein S7-AV [auth SU]185Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S8-AW [auth SV]188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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40S ribosomal protein S9-AX [auth SW]185Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S11-AY [auth SX]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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40S ribosomal protein S13Z [auth SY]150Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S14-BAA [auth SZ]128Saccharomyces cerevisiae S288CMutation(s): 0 
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40S ribosomal protein S21-ABA [auth Sa]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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40S ribosomal protein S22-ACA [auth Sb]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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40S ribosomal protein S23-ADA [auth Sc]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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40S ribosomal protein S24-AEA [auth Sd]134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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40S ribosomal protein S26-BFA [auth Se]97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
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40S ribosomal protein S27-AGA [auth Sf]81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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40S ribosomal protein S30-AHA [auth Sg]44Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Multiprotein-bridging factor 1IA [auth Sh]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MBF1SUF13YOR298C-A
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60S ribosomal protein L2-APA [auth LD]251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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60S ribosomal protein L3QA [auth LE]386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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60S ribosomal protein L4-ARA [auth LF]361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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60S ribosomal protein L5SA [auth LG]294Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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60S ribosomal protein L6-BTA [auth LH]167Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6BRPL16BRPL17BYL16BYLR448WL9324.4
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AUA [auth LI]222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 48
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60S ribosomal protein L8-AVA [auth LJ]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 49
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60S ribosomal protein L9-AWA [auth LK]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 50
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60S ribosomal protein L10XA [auth LL]218Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 51
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60S ribosomal protein L11-BYA [auth LM]169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 52
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60S ribosomal protein L13-AZA [auth LN]193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 53
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60S ribosomal protein L14-AAB [auth LO]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 54
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60S ribosomal protein L15-ABB [auth LP]203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 55
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60S ribosomal protein L16-ACB [auth LQ]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 56
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60S ribosomal protein L17-ADB [auth LR]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 57
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60S ribosomal protein L18-AEB [auth LS]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 58
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60S ribosomal protein L19-AFB [auth LT]188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 59
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60S ribosomal protein L20-AGB [auth LU]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 60
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60S ribosomal protein L21-AHB [auth LV]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 61
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60S ribosomal protein L22-AIB [auth LW]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 62
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60S ribosomal protein L23-AJB [auth LX]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 63
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60S ribosomal protein L24-AKB [auth LY]61Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 64
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60S ribosomal protein L25LB [auth LZ]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 65
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60S ribosomal protein L26-AMB [auth La]125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 66
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60S ribosomal protein L27-ANB [auth Lb]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 67
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60S ribosomal protein L28OB [auth Lc]148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 68
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60S ribosomal protein L29PB [auth Ld]58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 69
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60S ribosomal protein L30QB [auth Le]96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 70
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60S ribosomal protein L31-ARB [auth Lf]109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 71
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60S ribosomal protein L32SB [auth Lg]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 72
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60S ribosomal protein L33-ATB [auth Lh]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 73
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60S ribosomal protein L34-AUB [auth Li]112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 74
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60S ribosomal protein L35-AVB [auth Lj]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 75
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60S ribosomal protein L36-AWB [auth Lk]99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 76
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60S ribosomal protein L37-AXB [auth Ll]81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
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60S ribosomal protein L38YB [auth Lm]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 78
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60S ribosomal protein L39ZB [auth Ln]50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 79
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Ubiquitin-60S ribosomal protein L40AC [auth Lo]52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
UniProt
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Entity ID: 80
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60S ribosomal protein L41-BBC [auth Lp]25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41BRPL47BYL41BYDL133C-AYDL133BC
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Entity ID: 81
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60S ribosomal protein L42-ACC [auth Lq]103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 82
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60S ribosomal protein L43-ADC [auth Lr]91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 1
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TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequenceA [auth S2]1800Saccharomyces cerevisiae S288C
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Entity ID: 36
MoleculeChainsLengthOrganismImage
mRNA (32-MER)JA [auth S3]32Saccharomyces cerevisiae S288C
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Entity ID: 37
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tRNA (75-MER)KA [auth Sn]75Saccharomyces cerevisiae S288C
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Entity ID: 38
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tRNA (77-MER)LA [auth Sm]77Saccharomyces cerevisiae S288C
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Entity ID: 39
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25S rRNA (3184-MER)MA [auth LA]3394Saccharomyces cerevisiae S288C
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Entity ID: 40
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5S rRNA (121-MER)NA [auth LB]121Saccharomyces cerevisiae S288C
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Entity ID: 41
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5.8S rRNA (158-MER)OA [auth LC]158Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWI3285/8-1
German Research Foundation (DFG)GermanySPP-1879

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release