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- PDB-7nrd: Structure of the yeast Gcn1 bound to a colliding stalled 80S ribo... -

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Database: PDB / ID: 7nrd
TitleStructure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 40
  • 25S rRNA (3184-MER)
  • 5.8S rRNA (158-MER)
  • 5S rRNA (121-MER)
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Multiprotein-bridging factor 1
  • TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
  • mRNA (32-MER)
  • tRNA (75-MER)
  • tRNA (77-MER)
KeywordsRIBOSOME / Disome / GCN1 / Translation / GAAC / MBF1
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / response to cycloheximide / invasive growth in response to glucose limitation / GDP-dissociation inhibitor activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / rRNA export from nucleus ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / response to cycloheximide / invasive growth in response to glucose limitation / GDP-dissociation inhibitor activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / rRNA export from nucleus / preribosome, large subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / preribosome, small subunit precursor / ribonucleoprotein complex assembly / mRNA destabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / rescue of stalled ribosome / negative regulation of mRNA splicing, via spliceosome / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / maturation of SSU-rRNA / regulation of translational fidelity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / ribosomal small subunit biogenesis / protein kinase A catalytic subunit binding / maturation of LSU-rRNA / positive regulation of protein kinase activity / cellular response to amino acid starvation / ribosome assembly / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / positive regulation of translational fidelity / translational termination / protein kinase C binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / macroautophagy / protein tag / rRNA processing / large ribosomal subunit rRNA binding / cytoplasmic stress granule / cytoplasmic translation / cytosolic large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / protein localization / negative regulation of translation / ribosome / rRNA binding / transcription coactivator activity / structural constituent of ribosome / protein ubiquitination / translation / negative regulation of gene expression / positive regulation of protein phosphorylation / mRNA binding / G protein-coupled receptor signaling pathway / response to antibiotic / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Helix-turn-helix / Ribosomal protein S4/S9 / Ribosomal protein S19/S15, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / in:ipr023106: / Ribosomal protein S15P / Ribosomal protein L30e, conserved site ...Helix-turn-helix / Ribosomal protein S4/S9 / Ribosomal protein S19/S15, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / in:ipr023106: / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L31e domain superfamily / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L18e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein S9, conserved site / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S7, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S8 superfamily / Ribosomal protein L34e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L22/L17, conserved site / WD40-repeat-containing domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L19/L19e, domain 1 / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L21e, conserved site / Ribosomal protein L27e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S8e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S6e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S4e, central region / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L37ae protein family
40S ribosomal protein S3 / 40S ribosomal protein S13 / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S19-A / 40S ribosomal protein S21-A / gb:940534893: / 60S ribosomal protein L22-A / 40S ribosomal protein S22-A / 60S ribosomal protein L15-A / 60S ribosomal protein L7-A ...40S ribosomal protein S3 / 40S ribosomal protein S13 / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S19-A / 40S ribosomal protein S21-A / gb:940534893: / 60S ribosomal protein L22-A / 40S ribosomal protein S22-A / 60S ribosomal protein L15-A / 60S ribosomal protein L7-A / 40S ribosomal protein S9-A / Multiprotein-bridging factor 1 / 60S ribosomal protein L28 / 60S ribosomal protein L24-A / 60S ribosomal protein L25 / 60S ribosomal protein L39 / 60S ribosomal protein L9-A / 60S ribosomal protein L29 / 60S ribosomal protein L6-B / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L33-A / gb:831416132: / 60S ribosomal protein L36-A / gb:834774822: / gb:176433: / 60S ribosomal protein L27-A / 60S ribosomal protein L2-A / 60S ribosomal protein L3 / 60S ribosomal protein L30 / 60S ribosomal protein L4-A / 60S ribosomal protein L41-B / 60S ribosomal protein L35-A / 60S ribosomal protein L19-A / 40S ribosomal protein S18-A / 40S ribosomal protein S16-A / 60S ribosomal protein L18-A / 40S ribosomal protein S11-A / 60S ribosomal protein L23-A / 60S ribosomal protein L8-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S30-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 60S ribosomal protein L42-A / 60S ribosomal protein L43-A / 60S ribosomal protein L20-A / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L31-A / 40S ribosomal protein S17-B / 40S ribosomal protein S2 / tpg:329138943: / 40S ribosomal protein S29-A / 40S ribosomal protein S28-A / 40S ribosomal protein S25-A / 60S ribosomal protein L11-B / 60S ribosomal protein L13-A / 40S ribosomal protein S10-A / 60S ribosomal protein L21-A / 40S ribosomal protein S15 / 60S ribosomal protein L34-A / 60S ribosomal protein L38 / 60S ribosomal protein L37-A / 60S ribosomal protein L10 / 40S ribosomal protein S26-B / 60S ribosomal protein L5 / 40S ribosomal protein S14-B / 40S ribosomal protein S20 / 60S ribosomal protein L32 / Guanine nucleotide-binding protein subunit beta-like protein / 60S ribosomal protein L14-A / 40S ribosomal protein S27-A / 40S ribosomal protein S1-A / 40S ribosomal protein S0-A / 40S ribosomal protein S7-A / 60S ribosomal protein L16-A / 40S ribosomal protein S5 / 40S ribosomal protein S12
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.36 Å
AuthorsPochopien, A.A. / Beckert, B. / Wilson, D.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/8-1 Germany
German Research Foundation (DFG)SPP-1879 Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structure of Gcn1 bound to stalled and colliding 80S ribosomes.
Authors: Agnieszka A Pochopien / Bertrand Beckert / Sergo Kasvandik / Otto Berninghausen / Roland Beckmann / Tanel Tenson / Daniel N Wilson /
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 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
S2: TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence
SA: 40S ribosomal protein S3
SB: 40S ribosomal protein S5
SC: 40S ribosomal protein S10-A
SD: 40S ribosomal protein S12
SE: 40S ribosomal protein S15
SF: 40S ribosomal protein S16-A
SG: 40S ribosomal protein S17-B
SH: 40S ribosomal protein S18-A
SI: 40S ribosomal protein S19-A
SJ: 40S ribosomal protein S20
SK: 40S ribosomal protein S25-A
SL: 40S ribosomal protein S28-A
SM: 40S ribosomal protein S29-A
SN: Ubiquitin-40S ribosomal protein S31
SO: Guanine nucleotide-binding protein subunit beta-like protein
SP: 40S ribosomal protein S0-A
SQ: 40S ribosomal protein S1-A
SR: 40S ribosomal protein S2
SS: 40S ribosomal protein S4-A
ST: 40S ribosomal protein S6-A
SU: 40S ribosomal protein S7-A
SV: 40S ribosomal protein S8-A
SW: 40S ribosomal protein S9-A
SX: 40S ribosomal protein S11-A
SY: 40S ribosomal protein S13
SZ: 40S ribosomal protein S14-B
Sa: 40S ribosomal protein S21-A
Sb: 40S ribosomal protein S22-A
Sc: 40S ribosomal protein S23-A
Sd: 40S ribosomal protein S24-A
Se: 40S ribosomal protein S26-B
Sf: 40S ribosomal protein S27-A
Sg: 40S ribosomal protein S30-A
Sh: Multiprotein-bridging factor 1
S3: mRNA (32-MER)
Sn: tRNA (75-MER)
Sm: tRNA (77-MER)
LA: 25S rRNA (3184-MER)
LB: 5S rRNA (121-MER)
LC: 5.8S rRNA (158-MER)
LD: 60S ribosomal protein L2-A
LE: 60S ribosomal protein L3
LF: 60S ribosomal protein L4-A
LG: 60S ribosomal protein L5
LH: 60S ribosomal protein L6-B
LI: 60S ribosomal protein L7-A
LJ: 60S ribosomal protein L8-A
LK: 60S ribosomal protein L9-A
LL: 60S ribosomal protein L10
LM: 60S ribosomal protein L11-B
LN: 60S ribosomal protein L13-A
LO: 60S ribosomal protein L14-A
LP: 60S ribosomal protein L15-A
LQ: 60S ribosomal protein L16-A
LR: 60S ribosomal protein L17-A
LS: 60S ribosomal protein L18-A
LT: 60S ribosomal protein L19-A
LU: 60S ribosomal protein L20-A
LV: 60S ribosomal protein L21-A
LW: 60S ribosomal protein L22-A
LX: 60S ribosomal protein L23-A
LY: 60S ribosomal protein L24-A
LZ: 60S ribosomal protein L25
La: 60S ribosomal protein L26-A
Lb: 60S ribosomal protein L27-A
Lc: 60S ribosomal protein L28
Ld: 60S ribosomal protein L29
Le: 60S ribosomal protein L30
Lf: 60S ribosomal protein L31-A
Lg: 60S ribosomal protein L32
Lh: 60S ribosomal protein L33-A
Li: 60S ribosomal protein L34-A
Lj: 60S ribosomal protein L35-A
Lk: 60S ribosomal protein L36-A
Ll: 60S ribosomal protein L37-A
Lm: 60S ribosomal protein L38
Ln: 60S ribosomal protein L39
Lo: Ubiquitin-60S ribosomal protein L40
Lp: 60S ribosomal protein L41-B
Lq: 60S ribosomal protein L42-A
Lr: 60S ribosomal protein L43-A


Theoretical massNumber of molelcules
Total (without water)3,082,67082
Polymers3,082,67082
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 7 types, 7 molecules S2S3SnSmLALBLC

#1: RNA chain TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: TPG: 329138943
#36: RNA chain mRNA (32-MER)


Mass: 9885.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#37: RNA chain tRNA (75-MER)


Mass: 24222.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 176433
#38: RNA chain tRNA (77-MER)


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#39: RNA chain 25S rRNA (3184-MER)


Mass: 1096842.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416132
#40: RNA chain 5S rRNA (121-MER)


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 834774822
#41: RNA chain 5.8S rRNA (158-MER)


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 940534893

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40S ribosomal protein ... , 31 types, 31 molecules SASBSCSDSESFSGSHSISJSKSLSMSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSeSfSg

#2: Protein 40S ribosomal protein S3 / / RP13 / Small ribosomal subunit protein uS3 / YS3


Mass: 24702.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05750
#3: Protein 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26783
#4: Protein 40S ribosomal protein S10-A / Ribosome / Small ribosomal subunit protein eS10-A


Mass: 11042.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q08745
#5: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 13327.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P48589
#6: Protein 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 13421.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q01855
#7: Protein 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX51
#8: Protein 40S ribosomal protein S17-B / Ribosome / RP51B / Small ribosomal subunit protein eS17-B


Mass: 14268.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P14127
#9: Protein 40S ribosomal protein S18-A / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 16940.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX55
#10: Protein 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P07280
#11: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 11476.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38701
#12: Protein 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 7930.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q3E792
#13: Protein 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q3E7X9
#14: Protein 40S ribosomal protein S29-A / Ribosome / S36 / Small ribosomal subunit protein uS14-A / YS29


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P41057
#17: Protein 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 22811.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P32905
#18: Protein 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 24498.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P33442
#19: Protein 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 23212.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P25443
#20: Protein 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29338.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX35
#21: Protein 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 24965.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX37
#22: Protein 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21071.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26786
#23: Protein 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 21147.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX39
#24: Protein 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 21210.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: O13516
#25: Protein 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 16588.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX47
#26: Protein 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05756
#27: Protein 40S ribosomal protein S14-B / Ribosome / RP59B / Small ribosomal subunit protein uS11-B


Mass: 13560.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P39516
#28: Protein 40S ribosomal protein S21-A / Ribosome / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C0V8
#29: Protein 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C0W1
#30: Protein 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 15942.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX29
#31: Protein 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX31
#32: Protein 40S ribosomal protein S26-B / Ribosome / Small ribosomal subunit protein eS26-B


Mass: 11022.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P39939
#33: Protein 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P35997
#34: Protein/peptide 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


Mass: 5054.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX33

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Protein , 4 types, 4 molecules SNSOShLo

#15: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8329.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05759
#16: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34151.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38011
#35: Protein Multiprotein-bridging factor 1 / Suppressor of frameshift mutations protein 13


Mass: 13247.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: O14467
#79: Protein Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CH08

+
60S ribosomal protein ... , 40 types, 40 molecules LDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLg...

#42: Protein 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27089.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX45
#43: Protein 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P14126
#44: Protein 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P10664
#45: Protein 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33415.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26321
#46: Protein 60S ribosomal protein L6-B / Ribosome / L17 / Large ribosomal subunit protein eL6-B / RP18 / YL16


Mass: 18935.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05739
#47: Protein 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 25240.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05737
#48: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P17076
#49: Protein 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05738
#50: Protein 60S ribosomal protein L10 / / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI- ...L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25080.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P41805
#51: Protein 60S ribosomal protein L11-B / Ribosome / L16 / Large ribosomal subunit protein uL5-B / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q3E757
#52: Protein 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 21885.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q12690
#53: Protein 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 14976.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P36105
#54: Protein 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05748
#55: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26784
#56: Protein 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05740
#57: Protein 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX49
#58: Protein 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX82
#59: Protein 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20347.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX23
#60: Protein 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18148.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q02753
#61: Protein 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05749
#62: Protein 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14362.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX41
#63: Protein 60S ribosomal protein L24-A / Ribosome / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 7214.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04449
#64: Protein 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04456
#65: Protein 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14005.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05743
#66: Protein 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15437.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C2H6
#67: Protein 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P02406
#68: Protein 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43


Mass: 6560.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05747
#69: Protein 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 10487.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P14120
#70: Protein 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C2H8
#71: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14478.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38061
#72: Protein 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05744
#73: Protein 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 12608.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P87262
#74: Protein 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13811.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX84
#75: Protein 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11020.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05745
#76: Protein 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9229.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P49166
#77: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8714.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P49167
#78: Protein/peptide 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6227.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04650
#80: Protein/peptide 60S ribosomal protein L41-B / Ribosome / L47 / Large ribosomal subunit protein eL41-B / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX87
#81: Protein 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 11840.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX27
#82: Protein 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 9981.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX25

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Structure of the yeast Gcn1-bound coilliding stalled 80S ribosome with MBF1, Gir2, A/P-tRNA and P/E-tRNA
Type: RIBOSOME / Entity ID: #1-#82 / Source: NATURAL
Molecular weightExperimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
12RELION33D reconstruction
13PHENIX1.11.1-2575model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30016 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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