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- PDB-6woo: CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, ... -

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Basic information

Entry
Database: PDB / ID: 6woo
TitleCryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP
Components
  • (uS19) x 2
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal rRNA
  • 5S ribosomal RNA
  • L10
  • Met-tRNA-iMet
  • RACK1Receptor for activated C kinase 1
  • eIF5B
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL6
  • eL8
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • mRNAMessenger RNA
  • uL1
  • uL10
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
KeywordsRIBOSOME / yeast / initiation / eIF5B / GDP / Met-tRNAiMet
Function / homology
Function and homology information


protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of cellular response to stress / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of translational initiation / invasive growth in response to glucose limitation / GDP-dissociation inhibitor activity ...protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of cellular response to stress / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of translational initiation / 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, small subunit precursor / preribosome, large subunit precursor / mRNA destabilization / response to cycloheximide / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rescue of stalled ribosome / ribonucleoprotein complex assembly / rRNA methylation / negative regulation of mRNA splicing, via spliceosome / ribosomal large subunit export from nucleus / 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) / 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) / small-subunit processome / ribosomal large subunit biogenesis / protein kinase A catalytic subunit binding / translation initiation factor binding / ribosomal small subunit biogenesis / cellular response to amino acid starvation / positive regulation of protein kinase activity / mature ribosome assembly / maturation of LSU-rRNA / translational termination / translation initiation factor activity / ribosome assembly / DNA-(apurinic or apyrimidinic site) endonuclease activity / assembly of large subunit precursor of preribosome / positive regulation of translational fidelity / maintenance of translational fidelity / protein kinase C binding / protein localization / small ribosomal subunit rRNA 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 / mRNA 5'-UTR binding / macroautophagy / protein tag / rRNA processing / large ribosomal subunit rRNA binding / cytoplasmic stress granule / cytoplasmic translation / ribosome biogenesis / cytosolic large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / cytosolic small ribosomal subunit / 5S rRNA binding / small ribosomal subunit / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / protein ubiquitination / translation / GTPase activity / negative regulation of gene expression / positive regulation of protein phosphorylation / mRNA binding / G protein-coupled receptor signaling pathway / GTP binding / nucleolus / ubiquitin protein ligase binding / enzyme binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L1, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily ...Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L1, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / 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 L1-like / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / Translation initiation factor IF- 2, domain 3 / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L29/L35 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S8 superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L19/L19e superfamily / 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 / 60S acidic ribosomal protein P0 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S15P / Ribosomal protein L5 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L22/L17, 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 L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein S3Ae, 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 L34e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S7, conserved site / Ribosomal protein L2, conserved site / 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 S9, conserved site / Ribosomal protein S8e, conserved site / G-protein beta WD-40 repeat / 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
gb:1039024045: / gb:176433: / gb:1329886537: / gb:1675231216: / 60S ribosomal protein L38 / 40S ribosomal protein S28-A / 60S ribosomal protein L42-A / 40S ribosomal protein S22-A / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A ...gb:1039024045: / gb:176433: / gb:1329886537: / gb:1675231216: / 60S ribosomal protein L38 / 40S ribosomal protein S28-A / 60S ribosomal protein L42-A / 40S ribosomal protein S22-A / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L20-A / 60S ribosomal protein L43-A / 40S ribosomal protein S23-A / 40S ribosomal protein S19-A / 40S ribosomal protein S24-A / 40S ribosomal protein S30-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 60S ribosomal protein L23-A / 60S ribosomal protein L1-A / 40S ribosomal protein S21-A / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S11-A / 60S ribosomal protein L17-A / RPS5 isoform 1 / 60S ribosomal protein L28 / 60S ribosomal protein L24-A / 60S ribosomal protein L39 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L7-A / 60S ribosomal protein L26-A / 40S ribosomal protein S13 / 60S ribosomal protein L33-A / 60S ribosomal protein L36-A / 60S ribosomal protein L29 / 60S ribosomal protein L15-A / 60S ribosomal protein L22-A / 40S ribosomal protein S3 / 40S ribosomal protein S9-B / 60S ribosomal protein L2-A / 60S ribosomal protein L18-A / 40S ribosomal protein S25-A / 60S ribosomal protein L37-A / Eukaryotic translation initiation factor 5B / 40S ribosomal protein S26-B / 40S ribosomal protein S29-A / 60S ribosomal protein L10 / 40S ribosomal protein S0-B / 40S ribosomal protein S12 / 60S ribosomal protein L9-B / 40S ribosomal protein S20 / 60S ribosomal protein L34-A / 40S ribosomal protein S15 / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / 40S ribosomal protein S10-A / 60S ribosomal protein L13-A / 60S ribosomal protein L11-B / 40S ribosomal protein S14-B / 60S ribosomal protein L32 / 40S ribosomal protein S16-A / 40S ribosomal protein S17-B / 40S ribosomal protein S18-A / 60S ribosomal protein L19-A / 60S ribosomal protein L35-A / 60S ribosomal protein L4-A / 60S ribosomal protein L30 / 60S ribosomal protein L3 / 60S ribosomal protein L8-A / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S1-B / 40S ribosomal protein S2 / 60S ribosomal protein L5 / 60S ribosomal protein L16-A / 40S ribosomal protein S7-A / 40S ribosomal protein S27-A / 60S ribosomal protein L14-A / 60S ribosomal protein L25
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang, J. / Wang, J. / Puglisi, J. / Fernandez, I.S.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex.
Authors: Jinfan Wang / Jing Wang / Byung-Sik Shin / Joo-Ran Kim / Thomas E Dever / Joseph D Puglisi / Israel S Fernández /
Abstract: Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the ...Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNA on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNA immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal rRNA
A: uL2
B: uL3
C: uL4
D: uL18
E: eL6
F: uL30
G: eL8
H: uL6
I: uL16
J: uL5
L: eL13
M: eL14
N: eL15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: uL14
W: eL24
X: uL23
Y: uL24
Z: eL27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: eL36
j: eL37
k: eL38
l: eL39
m: eL40
n: eL41
o: eL42
p: eL43
q: uL1
r: uL10
K: L10
AA: uS2
BB: eS1
CC: uS5
DD: uS3
EE: eS4
FF: uS7
GG: eS6
HH: eS7
II: eS8
JJ: uS4
KK: eS10
LL: uS17
MM: eS12
NN: uS15
OO: uS11
PP: uS19
QQ: uS19
RR: eS17
SS: uS13
TT: eS19
UU: uS10
VV: eS21
WW: uS8
XX: uS12
YY: eS24
ZZ: eS25
aa: eS26
bb: eS27
cc: eS28
dd: uS14
ee: eS30
ff: eS31
gg: RACK1
2: 18S ribosomal RNA
1: eIF5B
3: Met-tRNA-iMet
4: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,121,30193
Polymers3,120,15384
Non-polymers1,1489
Water0
1


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

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Components

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RNA chain , 6 types, 6 molecules 578234

#1: RNA chain 25S ribosomal RNA /


Mass: 1057318.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#2: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039024045
#3: RNA chain 5.8S ribosomal rRNA


Mass: 50376.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1675231216
#81: RNA chain 18S ribosomal RNA /


Mass: 578475.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1329886537
#83: RNA chain Met-tRNA-iMet


Mass: 24583.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 176433
#84: RNA chain mRNA / Messenger RNA


Mass: 1923.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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Protein , 76 types, 76 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#4: Protein uL2


Mass: 26858.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX45
#5: Protein uL3


Mass: 43491.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#6: Protein uL4


Mass: 38825.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#7: Protein uL18


Mass: 33562.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#8: Protein eL6


Mass: 19869.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#9: Protein uL30


Mass: 25240.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#10: Protein eL8


Mass: 25814.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#11: Protein uL6


Mass: 21691.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P51401
#12: Protein uL16


Mass: 24937.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41805
#13: Protein uL5


Mass: 19136.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E757
#14: Protein eL13


Mass: 22472.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#15: Protein eL14


Mass: 14992.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#16: Protein eL15 / List of Subaru engines


Mass: 24221.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#17: Protein uL13


Mass: 22028.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#18: Protein uL22


Mass: 20245.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#19: Protein eL18


Mass: 20421.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#20: Protein eL19


Mass: 21631.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#21: Protein eL20


Mass: 20138.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#22: Protein eL21 /


Mass: 18034.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#23: Protein eL22


Mass: 11263.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#24: Protein uL14


Mass: 14005.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#25: Protein eL24


Mass: 7253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449
#26: Protein uL23


Mass: 13771.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#27: Protein uL24


Mass: 14063.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#28: Protein eL27


Mass: 15366.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#29: Protein uL15


Mass: 16559.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#30: Protein eL29


Mass: 6489.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05747
#31: Protein eL30


Mass: 10558.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#32: Protein eL31


Mass: 12292.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#33: Protein eL32 / CD59


Mass: 14022.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#34: Protein eL33


Mass: 11932.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#35: Protein eL34 /


Mass: 13671.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#36: Protein uL29


Mass: 13540.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#37: Protein eL36


Mass: 10918.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#38: Protein eL37


Mass: 9629.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#39: Protein eL38


Mass: 8643.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#41: Protein eL40


Mass: 5919.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CH08
#43: Protein eL42


Mass: 11655.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX27
#44: Protein eL43


Mass: 9611.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25
#45: Protein uL1


Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX43
#46: Protein uL10


Mass: 21474.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05317
#47: Protein L10


Mass: 12953.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#48: Protein uS2


Mass: 22852.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P46654
#49: Protein eS1


Mass: 24410.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P23248
#50: Protein uS5


Mass: 23212.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25443
#51: Protein uS3


Mass: 24702.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05750
#52: Protein eS4


Mass: 29039.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX35
#53: Protein uS7


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A0A1L4AA68
#54: Protein eS6


Mass: 25895.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX37
#55: Protein eS7


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26786
#56: Protein eS8


Mass: 22406.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX39
#57: Protein uS4


Mass: 20965.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05755
#58: Protein eS10


Mass: 11585.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q08745
#59: Protein uS17


Mass: 16561.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX47
#60: Protein eS12


Mass: 13327.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P48589
#61: Protein uS15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05756
#62: Protein uS11


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39516
#63: Protein uS19


Mass: 11651.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q01855
#64: Protein uS19


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX51
#65: Protein eS17


Mass: 14110.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14127
#66: Protein uS13


Mass: 15928.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX55
#67: Protein eS19


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P07280
#68: Protein uS10


Mass: 12076.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38701
#69: Protein eS21


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0V8
#70: Protein uS8


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W1
#71: Protein uS12


Mass: 15986.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX29
#72: Protein eS24


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX31
#73: Protein eS25


Mass: 8001.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E792
#74: Protein eS26


Mass: 11022.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39939
#75: Protein eS27


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35997
#76: Protein eS28


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E7X9
#77: Protein uS14


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41057
#78: Protein eS30


Mass: 6084.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX33
#79: Protein eS31


Mass: 6457.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05759
#80: Protein RACK1 / Receptor for activated C kinase 1


Mass: 34710.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38011
#82: Protein eIF5B /


Mass: 67068.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: FUN12, YAL035W / Production host: Escherichia coli (E. coli) / References: UniProt: P39730, protein-synthesizing GTPase

-
Protein/peptide , 2 types, 2 molecules ln

#40: Protein/peptide eL39


Mass: 6114.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#42: Protein/peptide eL41


Mass: 3137.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

-
Non-polymers , 4 types, 9 molecules

#85: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#86: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#87: Chemical ChemComp-U6A / N-carboxy-L-threonine


Type: L-peptide NH3 amino terminus / Mass: 163.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO5
#88: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 80S ribosome with eIF5B, Met-tRNAiMet, mRNA, and GDP / Type: RIBOSOME / Entity ID: #1-#84 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimera2model fitting
12RELION3.13D reconstruction
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4V8Y

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