PDB-8k2d: Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF...

Basic information

• Entry: Database: PDB / ID: 8k2d
• Title: Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A

Components

• (40S ribosomal protein ...) x 14
• (Large ribosomal subunit protein ...) x 43
• (Small ribosomal subunit protein ...) x 18
• (Ubiquitin-ribosomal protein ...) x 2
• 18S rRNA
• 23S rRNA
• 5.8S rRNA
• 5S rRNA
• Elongation factor 2
• Eukaryotic translation initiation factor 5A-1
• Suppressor protein STM1

• Keywords: RIBOSOME / 80S ribosome / tigecycline / antibiotic

Function / homology

Function:

cytoplasmic translational elongation through polyproline stretches / positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / cytoplasmic translational elongation / positive regulation of translational termination / Peptide chain elongation / triplex DNA binding / Synthesis of diphthamide-EEF2 / ribosome hibernation / cytoplasmic translational termination / translation elongation factor binding / Platelet degranulation / positive regulation of translational elongation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nonfunctional rRNA decay / response to cycloheximide / telomeric DNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of translational initiation / translational elongation / regulation of amino acid metabolic process / ribosomal large subunit export from nucleus / positive regulation of protein kinase activity / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / 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) / translation elongation factor activity / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translational termination / ribosomal small subunit export from nucleus / maturation of LSU-rRNA / translation regulator activity / translation repressor activity / rescue of stalled ribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / translation initiation factor activity / telomere maintenance / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome assembly / protein kinase C binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / cytoplasmic stress granule / ribosome biogenesis / ribosome binding / protein-folding chaperone binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit

Domain/homology:

Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / S27a-like superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S10, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L19/L19e conserved site / : / : / Ribosomal protein L19e signature. / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein S17e, conserved site / Ribosomal protein L44 / Ribosomal protein S17e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S27a

Component:

GUANOSINE-5'-DIPHOSPHATE / TIGECYCLINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Eukaryotic translation initiation factor 5A-1 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Elongation factor 2 / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Suppressor protein STM1 / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A

• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Buschauer, R. / Beckmann, R. / Cheng, J.

Funding support

1items

Organization	Grant number	Country
Not funded

• Citation: Journal: Nat Commun / Year: 2024; Title: Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.; Authors: Xiang Li / Mengjiao Wang / Timo Denk / Robert Buschauer / Yi Li / Roland Beckmann / Jingdong Cheng / ; Abstract: Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, even though it is also cytotoxic for human cells, the molecular mechanism of its inhibition remains unclear. Here, we present cryo-EM structures of tigecycline-bound human mitochondrial 55S, 39S, cytoplasmic 80S and yeast cytoplasmic 80S ribosomes. We find that at clinically relevant concentrations, tigecycline effectively targets human 55S mitoribosomes, potentially, by hindering A-site tRNA accommodation and by blocking the peptidyl transfer center. In contrast, tigecycline does not bind to human 80S ribosomes under physiological concentrations. However, at high tigecycline concentrations, in addition to blocking the A-site, both human and yeast 80S ribosomes bind tigecycline at another conserved binding site restricting the movement of the L1 stalk. In conclusion, the observed distinct binding properties of tigecycline may guide new pathways for drug design and therapy.

History

Deposition	Jul 12, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Data collection / Structure summary Category: em_admin / pdbx_entry_details / pdbx_modification_feature Item: _em_admin.last_update

Assembly

Deposited unit

C2: 18S rRNA

C1: 23S rRNA

C4: 5S rRNA

C3: 5.8S rRNA

SA: Small ribosomal subunit protein uS2A

SB: 40S ribosomal protein S1-A

SC: 40S ribosomal protein S2

SD: Small ribosomal subunit protein uS3

SE: 40S ribosomal protein S4-A

SF: Small ribosomal subunit protein uS7

SG: 40S ribosomal protein S6-A

SH: 40S ribosomal protein S7-A

SI: 40S ribosomal protein S8-A

SJ: 40S ribosomal protein S9-A

SK: Small ribosomal subunit protein eS10A

SL: Small ribosomal subunit protein uS17A

SM: Small ribosomal subunit protein eS12

SN: 40S ribosomal protein S13

SO: 40S ribosomal protein S14-A

SP: Small ribosomal subunit protein uS19

SQ: Small ribosomal subunit protein uS9A

SR: Small ribosomal subunit protein eS17A

SS: Small ribosomal subunit protein uS13A

ST: Small ribosomal subunit protein eS19A

SU: Small ribosomal subunit protein uS10

SV: Small ribosomal subunit protein eS21A

SW: 40S ribosomal protein S22-A

SX: 40S ribosomal protein S23-A

SY: 40S ribosomal protein S24-A

SZ: Small ribosomal subunit protein eS25A

Sa: Small ribosomal subunit protein eS26B

Sb: 40S ribosomal protein S27-A

Sc: Small ribosomal subunit protein eS28A

Sd: Small ribosomal subunit protein uS14A

Se: 40S ribosomal protein S30-A

Sf: Ubiquitin-ribosomal protein eS31 fusion protein

Sg: Small ribosomal subunit protein RACK1

LA: Large ribosomal subunit protein uL2A

LB: Large ribosomal subunit protein uL3

LC: Large ribosomal subunit protein uL4A

LD: Large ribosomal subunit protein uL18

LE: Large ribosomal subunit protein eL6A

LF: Large ribosomal subunit protein uL30A

LG: Large ribosomal subunit protein eL8A

LH: Large ribosomal subunit protein uL6A

LI: Large ribosomal subunit protein uL16

LJ: Large ribosomal subunit protein uL5A

LK: Large ribosomal subunit protein uL11A

LL: Large ribosomal subunit protein eL13A

LM: Large ribosomal subunit protein eL14A

LN: Large ribosomal subunit protein eL15A

LO: Large ribosomal subunit protein uL13A

LP: Large ribosomal subunit protein uL22A

LQ: Large ribosomal subunit protein eL18A

LR: Large ribosomal subunit protein eL19A

LS: Large ribosomal subunit protein eL20A

LT: Large ribosomal subunit protein eL21A

LU: Large ribosomal subunit protein eL22A

LV: Large ribosomal subunit protein uL14A

LW: Large ribosomal subunit protein eL24A

LX: Large ribosomal subunit protein uL23

LY: Large ribosomal subunit protein uL24A

LZ: Large ribosomal subunit protein eL27A

La: Large ribosomal subunit protein uL15

Lb: Large ribosomal subunit protein eL29

Lc: Large ribosomal subunit protein eL30

Ld: Large ribosomal subunit protein eL31A

Le: Large ribosomal subunit protein eL32

Lf: Large ribosomal subunit protein eL33A

Lg: Large ribosomal subunit protein eL34A

Lh: Large ribosomal subunit protein uL29A

Li: Large ribosomal subunit protein eL36A

Lj: Large ribosomal subunit protein eL37A

Lk: Large ribosomal subunit protein eL38

Ll: Large ribosomal subunit protein eL39

Lm: Ubiquitin-ribosomal protein eL40A fusion protein

Ln: Large ribosomal subunit protein eL41A

Lo: Large ribosomal subunit protein eL42A

Lp: Large ribosomal subunit protein eL43A

CE: Eukaryotic translation initiation factor 5A-1

L1: Large ribosomal subunit protein uL1A

P0: Large ribosomal subunit protein uL10

CD: Elongation factor 2

CS: Suppressor protein STM1

hetero molecules

Summary:

• 3.33 MDa, 84 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	3,327,245	104
Polymers	3,322,590	84
Non-polymers	4,655	20
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author
• Evidence: electron microscopy, not applicable

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555		1

Components

RNA chain , 4 types, 4 molecules C2 C1 C4 C3

#1: RNA chain

C2 18S rRNA

Details:

Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

#2: RNA chain

C1 23S rRNA

Details:

Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822

#3: RNA chain

C4 5S rRNA / 5S rRNA

Details:

Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039024045

#4: RNA chain

C3 5.8S rRNA

Details:

Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1267176494

Small ribosomal subunit protein ... , 18 types, 18 molecules SA SD SF SK SL SM SP SQ SR SS ST SU SV SZ Sa Sc Sd Sg

#5: Protein

SA Small ribosomal subunit protein uS2A / 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A

Details:

Mass: 28051.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905

#8: Protein

SD Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 / RP13 / YS3

Details:

Mass: 26542.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750

#10: Protein

SF Small ribosomal subunit protein uS7 / 40S ribosomal protein S5 / RP14 / S2 / YS8

Details:

Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783

#15: Protein

SK Small ribosomal subunit protein eS10A / 40S ribosomal protein S10-A

Details:

Mass: 12757.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08745

#16: Protein

SL Small ribosomal subunit protein uS17A / 40S ribosomal protein S11-A / RP41 / S18 / YS12

Details:

Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX47

#17: Protein

SM Small ribosomal subunit protein eS12 / 40S ribosomal protein S12

Details:

Mass: 15488.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48589

#20: Protein

SP Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21

Details:

Mass: 16031.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855

#21: Protein

SQ Small ribosomal subunit protein uS9A / 40S ribosomal protein S16-A / RP61R

Details:

Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX51

#22: Protein

SR Small ribosomal subunit protein eS17A / 40S ribosomal protein S17-A / RP51A

Details:

Mass: 15820.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02407

#23: Protein

SS Small ribosomal subunit protein uS13A / 40S ribosomal protein S18-A

Details:

Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX55

#24: Protein

ST Small ribosomal subunit protein eS19A / 40S ribosomal protein S19-A / RP55A / S16a / YP45 / YS16A

Details:

Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280

#25: Protein

SU Small ribosomal subunit protein uS10 / 40S ribosomal protein S20

Details:

Mass: 13929.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701

#26: Protein

SV Small ribosomal subunit protein eS21A / 40S ribosomal protein S21-A / S26 / YS25

Details:

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

#30: Protein

SZ Small ribosomal subunit protein eS25A / 40S ribosomal protein S25-A / RP45 / S31 / YS23

Details:

Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792

#31: Protein

Sa Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B

Details:

Mass: 13480.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39939

#33: Protein

Sc Small ribosomal subunit protein eS28A / 40S ribosomal protein S28-A / S33 / YS27

Details:

Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9

#34: Protein

Sd Small ribosomal subunit protein uS14A / 40S ribosomal protein S29-A / S36 / YS29

Details:

Mass: 6675.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057

#37: Protein

Sg Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1

Details:

Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011

40S ribosomal protein ... , 14 types, 14 molecules SB SC SE SG SH SI SJ SN SO SW SX SY Sb Se

#6: Protein

SB 40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A

Details:

Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33442

#7: Protein

SC 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5

Details:

Mass: 27490.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443

#9: Protein

SE 40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6

Details:

Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX35

#11: Protein

SG 40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4

Details:

Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37

#12: Protein

SH 40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A

Details:

Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26786

#13: Protein

SI 40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9

Details:

Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX39

#14: Protein

SJ 40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11

Details:

Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516

#18: Protein

SN 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15

Details:

Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756

#19: Protein

SO 40S ribosomal protein S14-A / RP59A / Small ribosomal subunit protein uS11-A

Details:

Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367

#27: Protein

SW 40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22

Details:

Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1

#28: Protein

SX 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14

Details:

Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX29

#29: Protein

SY 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A

Details:

Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31

#32: Protein

Sb 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20

Details:

Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35997

#35: Protein

Se 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A

Details:

Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX33

Ubiquitin-ribosomal protein ... , 2 types, 2 molecules Sf Lm

#36: Protein

Sf Ubiquitin-ribosomal protein eS31 fusion protein

Details:

Mass: 17254.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05759

#76: Protein

Lm Ubiquitin-ribosomal protein eL40A fusion protein

Details:

Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08

Large ribosomal subunit protein ... , 43 types, 43 molecules LA LB LC LD LE LF LG LH LI LJ LK LL LM LN LO LP LQ LR LS LT LU LV LW LX LY LZ La Lb Lc Ld ...

#38: Protein

LA Large ribosomal subunit protein uL2A / 60S ribosomal protein L2-A / L5 / RP8 / YL6

Details:

Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX45

#39: Protein

LB Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1

Details:

Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126

#40: Protein

LC Large ribosomal subunit protein uL4A / 60S ribosomal protein L4-A / L2 / RP2 / YL2

Details:

Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664

#41: Protein

LD Large ribosomal subunit protein uL18 / 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3

Details:

Mass: 33764.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321

#42: Protein

LE Large ribosomal subunit protein eL6A / 60S ribosomal protein L6-A / L17 / RP18 / YL16

Details:

Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326

#43: Protein

LF Large ribosomal subunit protein uL30A / 60S ribosomal protein L7-A / L6 / RP11 / YL8

Details:

Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737

#44: Protein

LG Large ribosomal subunit protein eL8A / 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5

Details:

Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076

#45: Protein

LH Large ribosomal subunit protein uL6A / 60S ribosomal protein L9-A / L8 / RP24 / YL11

Details:

Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738

#46: Protein

LI Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein

Details:

Mass: 25410.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805

#47: Protein

LJ Large ribosomal subunit protein uL5A / 60S ribosomal protein L11-A / L16 / RP39 / YL22

Details:

Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W9

#48: Protein

LK Large ribosomal subunit protein uL11A / 60S ribosomal protein L12-A / L15 / YL23

Details:

Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX53

#49: Protein

LL Large ribosomal subunit protein eL13A / 60S ribosomal protein L13-A

Details:

Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12690

#50: Protein

LM Large ribosomal subunit protein eL14A / 60S ribosomal protein L14-A

Details:

Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105

#51: Protein

LN Large ribosomal subunit protein eL15A / 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18

Details:

Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748

#52: Protein

LO Large ribosomal subunit protein uL13A / 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15

Details:

Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784

#53: Protein

LP Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A / L20A / YL17

Details:

Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740

#54: Protein

LQ Large ribosomal subunit protein eL18A / 60S ribosomal protein L18-A / RP28

Details:

Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49

#55: Protein

LR Large ribosomal subunit protein eL19A / 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14

Details:

Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX82

#56: Protein

LS Large ribosomal subunit protein eL20A / 60S ribosomal protein L20-A / L18a

Details:

Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23

#57: Protein

LT Large ribosomal subunit protein eL21A / 60S ribosomal protein L21-A

Details:

Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753

#58: Protein

LU Large ribosomal subunit protein eL22A / 60S ribosomal protein L22-A / L1c / RP4 / YL31

Details:

Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749

#59: Protein

LV Large ribosomal subunit protein uL14A / 60S ribosomal protein L23-A / L17a / YL32

Details:

Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41

#60: Protein

LW Large ribosomal subunit protein eL24A / 60S ribosomal protein L24-A / L30 / RP29 / YL21

Details:

Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449

#61: Protein

LX Large ribosomal subunit protein uL23 / 60S ribosomal protein L25 / RP16L / YL25 / YP42'

Details:

Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456

#62: Protein

LY Large ribosomal subunit protein uL24A / 60S ribosomal protein L26-A / L33 / YL33

Details:

Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743

#63: Protein

LZ Large ribosomal subunit protein eL27A / 60S ribosomal protein L27-A

Details:

Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6

#64: Protein

La Large ribosomal subunit protein uL15 / 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24

Details:

Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406

#65: Protein

Lb Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / YL43

Details:

Mass: 6691.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05747

#66: Protein

Lc Large ribosomal subunit protein eL30 / 60S ribosomal protein L30 / L32 / RP73 / YL38

Details:

Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120

#67: Protein

Ld Large ribosomal subunit protein eL31A / 60S ribosomal protein L31-A / L34 / YL28

Details:

Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8

#68: Protein

Le Large ribosomal subunit protein eL32 / 60S ribosomal protein L32

Details:

Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061

#69: Protein

Lf Large ribosomal subunit protein eL33A / 60S ribosomal protein L33-A / L37 / RP47 / YL37

Details:

Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744

#70: Protein

Lg Large ribosomal subunit protein eL34A / 60S ribosomal protein L34-A

Details:

Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262

#71: Protein

Lh Large ribosomal subunit protein uL29A / 60S ribosomal protein L35-A

Details:

Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX84

#72: Protein

Li Large ribosomal subunit protein eL36A / 60S ribosomal protein L36-A / L39 / YL39

Details:

Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745

#73: Protein

Lj Large ribosomal subunit protein eL37A / 60S ribosomal protein L37-A / L43 / YL35 / YP55

Details:

Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166

#74: Protein

Lk Large ribosomal subunit protein eL38 / 60S ribosomal protein L38

Details:

Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167

#75: Protein

Ll Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 / L46 / YL40

Details:

Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650

#77: Protein/peptide

Ln Large ribosomal subunit protein eL41A / 60S ribosomal protein L41-A / L47 / YL41

Details:

Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX86

#78: Protein

Lo Large ribosomal subunit protein eL42A / 60S ribosomal protein L42-A / L41 / YL27 / YP44

Details:

Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX27

#79: Protein

Lp Large ribosomal subunit protein eL43A / 60S ribosomal protein L43-A / L37a / YL35

Details:

Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX25

#81: Protein

L1 Large ribosomal subunit protein uL1A / 60S ribosomal protein L1-A / L10a

Details:

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

#82: Protein

P0 Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / A0 / L10e

Details:

Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317

Protein , 3 types, 3 molecules CE CD CS

#80: Protein

CE Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / Hypusine-containing protein HP2 / eIF-4D

Details:

Mass: 17222.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23301

#83: Protein

CD Elongation factor 2 / EF-2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase / Translation elongation factor 2

Details:

Mass: 93407.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32324, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

#84: Protein

CS Suppressor protein STM1 / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1

Details:

Mass: 30048.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39015

Non-polymers , 4 types, 20 molecules

#85: Chemical

C2-1901 SM-501 Sa-500 Sb-101 Lg-500 Lj-501 Lm-500 Lo-501 Lp-501
ChemComp-ZN / ZINC ION

Details:

Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

#86: Chemical

C1-3401 C1-3402 C1-3403 C1-3404 C1-3405 C1-3406
ChemComp-T1C / TIGECYCLINE

Details:

Mass: 587.665 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₉H₄₁N₅O₈ / Comment: medication, antibiotic*YM

#87: Chemical

C1-3407 C1-3408 C3-201 CD-901
ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

#88: Chemical

CD-902 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE

Details:

Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM

Details

• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: ELECTRON MICROSCOPY
• EM experiment: Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

• Component: Name: yeast 80S ribosome / Type: RIBOSOME / Entity ID: #1-#82, #84 / Source: NATURAL
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Buffer solution: pH: 7.4
• Specimen: Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Microscopy: Model: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
• Electron lens: Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
• Image recording: Electron dose: 44 e/Ų / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

Processing

• CTF correction: Details: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 3D reconstruction: Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105095 / Symmetry type: POINT