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- PDB-4v4b: Structure of the ribosomal 80S-eEF2-sordarin complex from yeast o... -

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Basic information

Entry
Database: PDB / ID: 4v4b
TitleStructure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 28
  • 18S ribosomal RNA
  • 5.8S/25S ribosomal RNA
  • 5S RIBOSOMAL RNA
  • Elongation factor 2EEF2
KeywordsRIBOSOME / 80S ribosome / 40S ribosomal subunit / eEF2 / tRNA translocation / sordarin / cryo-EM
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein hydroxylation / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein hydroxylation / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / 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) / regulation of translational fidelity / translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation elongation factor activity / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / small-subunit processome / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / protein-folding chaperone binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / GTPase activity / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Ribosomal protein S10, eukaryotic/archaeal ...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 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Tr-type G domain, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein S19A/S15e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L44e / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Ribosomal protein L44 / Ribosomal protein L23, N-terminal domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L31e, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein L19, eukaryotic / Ribosomal protein L44e signature. / Ribosomal protein L7A/L8 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L10e signature. / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal protein L6, conserved site-2 / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L19 / Ribosomal protein L32e, conserved site / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L24e-related / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal_L19e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L19e / Ribosomal protein L18e / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L37e / Ribosomal protein L24e / Elongation factor Tu domain 2 / Ribosomal L15
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / 40S ribosomal protein S22-A / 60S ribosomal protein L31-B / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL15A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L11-B / 60S ribosomal protein L18-A / 60S ribosomal protein L31-B / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2B / Small ribosomal subunit protein uS17B / Large ribosomal subunit protein eL18B / Small ribosomal subunit protein uS9B / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Elongation factor 2 / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / 40S ribosomal protein S18-A / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / 40S ribosomal protein S29-B / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein uL4B / 60S ribosomal protein L43-A / 60S ribosomal protein L1-B / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL21A / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein uS8B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsSpahn, C.M. / Gomez-Lorenzo, M.G. / Grassucci, R.A. / Jorgensen, R. / Andersen, G.R. / Beckmann, R. / Penczek, P.A. / Ballesta, J.P.G. / Frank, J.
Citation
Journal: EMBO J / Year: 2004
Title: Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Authors: Christian M T Spahn / Maria G Gomez-Lorenzo / Robert A Grassucci / Rene Jørgensen / Gregers R Andersen / Roland Beckmann / Pawel A Penczek / Juan P G Ballesta / Joachim Frank /
Abstract: An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and ...An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.
#1: Journal: Nat Struct Biol / Year: 1999
Title: EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome.
Authors: R K Agrawal / A B Heagle / P Penczek / R A Grassucci / J Frank /
Abstract: Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the ...Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the pretranslocational complex and for the completion of translocation. In addition, large conformational changes have been identified in the ribosome. The head of the 30S subunit shifts toward the L1 protein side, and the L7/L12 stalk becomes bifurcated upon EF-G binding. Upon GTP hydrolysis, the bifurcation is reversed and an arc-like connection is formed between the base of the stalk and EF-G.
#2: Journal: PROG.NUCLEIC ACID RES.MOL.BIOL. / Year: 1996
Title: The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery.
Authors: Ballesta, J.P. / Remacha, M.
#3: Journal: Science / Year: 2000
Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1S1I, 1S1H
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 18, 2015Group: Other
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Other / Category: atom_sites / em_image_scans / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND PDB ENTRIES 1S1H AND 1S1I REPRESENT ONE CRYO-EM STRUCTURE OF THE SACCHAROMYCES CEREVISIAE ...COMPOUND PDB ENTRIES 1S1H AND 1S1I REPRESENT ONE CRYO-EM STRUCTURE OF THE SACCHAROMYCES CEREVISIAE 80S RIBOSOME. THIS FILE, 1S1H, CONTAINS THE 40S SUBUNIT. THE 60S RIBOSOMAL SUBUNIT IS IN FILE 1S1I.

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Assembly

Deposited unit
AA: 18S ribosomal RNA
AT: Elongation factor 2
AB: 40S ribosomal protein S0-A
AC: 40S ribosomal protein S3
AD: 40S ribosomal protein S9-A
AE: 40S ribosomal protein S2
AG: 40S ribosomal protein S5
AH: 40S ribosomal protein S22
AI: 40S ribosomal protein S16
AJ: 40S ribosomal protein S20
AK: 40S ribosomal protein S14-A
AL: 40S ribosomal protein S23
AM: 40S ribosomal protein S18
AN: 40S ribosomal protein S29-B
AO: 40S ribosomal protein S13
AQ: 40S ribosomal protein S11
AS: 40S ribosomal protein S15
B3: 5.8S/25S ribosomal RNA
B4: 5S RIBOSOMAL RNA
BA: 60S ribosomal protein L1
BB: 60S ribosomal protein L2
BC: 60S ribosomal protein L3
BD: 60S ribosomal protein L4-B
BE: 60S ribosomal protein L5
BF: 60S ribosomal protein L7-A
BG: 60S ribosomal protein L8-A
BH: 60S ribosomal protein L9-A
BI: 60S ribosomal protein L10
BJ: 60S ribosomal protein L11
BK: 60S ribosomal protein L12
BL: 60S ribosomal protein L15-A
BM: 60S ribosomal protein L16-A
BN: 60S ribosomal protein L17-A
BO: 60S ribosomal protein L18
BP: 60S ribosomal protein L19
BQ: 60S ribosomal protein L21-A
BR: 60S ribosomal protein L23
BS: 60S ribosomal protein L24-A
BT: 60S ribosomal protein L25
BU: 60S ribosomal protein L26-A
BV: 60S ribosomal protein L28
B0: 60S ribosomal protein L32
BW: 60S ribosomal protein L31
BX: 60S ribosomal protein L35
BY: 60S ribosomal protein L37-A
BZ: 60S ribosomal protein L42
B9: 60S ribosomal protein L43


Theoretical massNumber of molelcules
Total (without water)2,305,21547
Polymers2,305,21547
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules AAB3B4

#1: RNA chain 18S ribosomal RNA /


Mass: 489331.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: modelled as analogous molecule of T. thermophilus taken from PDB entry 1FJF
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 155076
#18: RNA chain 5.8S/25S ribosomal RNA


Mass: 971012.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: REPRESENTED BY THE ANALOGOUS MOLECULE OF H. MARISMORTUI TAKEN FROM PDB ENTRY 1FFK AND SUPPLEMENTED WITH SEQUENCES FROM PDB ENTRIES 1MMS, 1MZP AND 1GIY
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 3377778
#19: RNA chain 5S RIBOSOMAL RNA /


Mass: 40298.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: REPRESENTED BY THE ANALOGOUS MOLECULE OF H. MARISMORTUI TAKEN FROM PDB ENTRY 1FFK
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 3377779

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Protein , 1 types, 1 molecules AT

#2: Protein Elongation factor 2 / EEF2 / EF-2


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

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40S ribosomal protein ... , 15 types, 15 molecules ABACADAEAGAHAIAJAKALAMANAOAQAS

#3: Protein 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A


Mass: 20355.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#4: Protein 40S ribosomal protein S3 / / YS3 / RP13


Mass: 21321.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750
#5: Protein 40S ribosomal protein S9-A / Ribosome / S13 / YS11 / RP21 / YP28


Mass: 20363.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#6: Protein 40S ribosomal protein S2 / / S4 / YS5 / RP12 / Omnipotent suppressor protein SUP44


Mass: 15639.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#7: Protein 40S ribosomal protein S5 / / S2 / YS8 / RP14


Mass: 16577.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783
#8: Protein 40S ribosomal protein S22 / / S24 / YS22 / RP50 / YP58


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04648, UniProt: Q3E7Y3*PLUS
#9: Protein 40S ribosomal protein S16 / / RP61R


Mass: 15746.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40213, UniProt: P0CX52*PLUS
#10: Protein 40S ribosomal protein S20 /


Mass: 11352.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#11: Protein 40S ribosomal protein S14-A / Ribosome / RP59A


Mass: 14459.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367
#12: Protein 40S ribosomal protein S23 / / S28 / YS14 / RP37


Mass: 12879.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32827, UniProt: P0CX30*PLUS
#13: Protein 40S ribosomal protein S18 /


Mass: 15485.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35271, UniProt: P0CX56*PLUS
#14: Protein/peptide 40S ribosomal protein S29-B / Ribosome / S36 / YS29


Mass: 4328.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41058
#15: Protein 40S ribosomal protein S13 / / S27A / YS15


Mass: 7841.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#16: Protein 40S ribosomal protein S11 / / S18 / YS12 / RP41


Mass: 8777.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26781, UniProt: P0CX48*PLUS
#17: Protein 40S ribosomal protein S15 / / S21 / YS21 / RP52 / RIG protein


Mass: 8901.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855

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60S ribosomal protein ... , 28 types, 28 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVB0BWBXBYBZB9

#20: Protein 60S ribosomal protein L1 / / L10a


Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53030, UniProt: P0CX43*PLUS
#21: Protein 60S ribosomal protein L2 / / YL6 / L5 / RP8


Mass: 27332.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05736, UniProt: P0CX46*PLUS
#22: Protein 60S ribosomal protein L3 / / YL1 / RP1 / Trichodermin resistance protein


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#23: Protein 60S ribosomal protein L4-B / Ribosome / L2B / RP2


Mass: 38997.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49626
#24: Protein 60S ribosomal protein L5 / / L1 / YL3 / Ribosomal 5S RNA-binding protein


Mass: 25444.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#25: Protein 60S ribosomal protein L7-A / Ribosome / L6A / YL8A / RP11


Mass: 18452.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#26: Protein 60S ribosomal protein L8-A / Ribosome / L7A-2 / L4-2 / YL5 / RP6


Mass: 12628.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#27: Protein 60S ribosomal protein L9-A / Ribosome / L8 / YL11 / RP25


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
#28: Protein 60S ribosomal protein L10 / / L9 / Ubiquinol-cytochrome C reductase complex subunit VI requiring protein


Mass: 19249.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805
#29: Protein 60S ribosomal protein L11 / / L16 / YL16 / 39A / RP39


Mass: 19624.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06380, UniProt: Q3E757*PLUS
#30: Protein 60S ribosomal protein L12 / / L15 / YL23


Mass: 13953.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17079, UniProt: P0CX53*PLUS
#31: Protein 60S ribosomal protein L15-A / Ribosome / YL10 / L13 / RP15R / YP18


Mass: 24351.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#32: Protein 60S ribosomal protein L16-A / Ribosome / L13A / RP22


Mass: 16483.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#33: Protein 60S ribosomal protein L17-A / Ribosome / YL17-A


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#34: Protein 60S ribosomal protein L18 / / RP28


Mass: 13129.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07279, UniProt: P0CX50*PLUS
#35: Protein 60S ribosomal protein L19 / / L23 / YL14 / RP33 / RP15L


Mass: 16318.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05735, UniProt: P0CX83*PLUS
#36: Protein 60S ribosomal protein L21-A / Ribosome


Mass: 11609.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#37: Protein 60S ribosomal protein L23 / / L17


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04451, UniProt: P0CX42*PLUS
#38: Protein 60S ribosomal protein L24-A / Ribosome / L30A / RP29 / YL21


Mass: 6550.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449
#39: Protein 60S ribosomal protein L25 / / YL25 / RP61L


Mass: 9480.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#40: Protein 60S ribosomal protein L26-A / Ribosome / YL33


Mass: 14134.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#41: Protein 60S ribosomal protein L28 / / L27A / L29 / YL24 / RP62


Mass: 16631.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#42: Protein 60S ribosomal protein L32 /


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
#43: Protein 60S ribosomal protein L31 / / L34 / YL28


Mass: 12848.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04649, UniProt: P0C2H9*PLUS
#44: Protein 60S ribosomal protein L35 /


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39741, UniProt: P0CX84*PLUS
#45: Protein 60S ribosomal protein L37-A / Ribosome / L35 / YP55


Mass: 9746.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#46: Protein 60S ribosomal protein L42 / / L44 / YL27 / YP44 / L41


Mass: 12115.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02405, UniProt: P0CX28*PLUS
#47: Protein 60S ribosomal protein L43 / / L37A / YL35


Mass: 9981.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49631, UniProt: P0CX26*PLUS

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeParent-IDDetails
1yeast 80S ribosomeEukaryotic ribosomeRIBOSOME0
2elongation factor 2EEF21protein-synthesizing GTPase activity
340S ribosomal protein S0-ARibosome1structural constituent of ribosome
440S ribosomal protein S31structural constituent of ribosome
540S ribosomal protein S9-ARibosome1structural constituent of ribosome
640S ribosomal protein S21structural constituent of ribosome
740S ribosomal protein S51structural constituent of ribosome
840S ribosomal protein S221structural constituent of ribosome
940S ribosomal protein S161structural constituent of ribosome
1040S ribosomal protein S201structural constituent of ribosome
1140S ribosomal protein S14-ARibosome1structural constituent of ribosome
1240S ribosomal protein S231structural constituent of ribosome
1340S ribosomal protein S181structural constituent of ribosome
1440S ribosomal protein S29-BRibosome1structural constituent of ribosome
1540S ribosomal protein S131structural constituent of ribosome
1640S ribosomal protein S111structural constituent of ribosome
1740S ribosomal protein S151structural constituent of ribosome
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20 / Date: Feb 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 52000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 4900 nm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: CTF correction of 3D-maps by Wiener filtration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D projection matching; conjugate gradients with regularization
Resolution: 11.7 Å / Actual pixel size: 2.93 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--manual fitting in O
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms20788 31507 0 0 52295

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