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- PDB-4v6i: Localization of the small subunit ribosomal proteins into a 6.1 A... -

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Entry
Database: PDB / ID: 4v6i
TitleLocalization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome
Components
  • (40S ribosomal protein ...) x 27
  • (60S acidic ribosomal protein ...) x 3
  • (60S ribosomal protein ...) x 43
  • (Unknown 40S ribosomal protein ...) x 2
  • (Unknown protein) x 2
  • 18S rRNA
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')
  • P-SITE TRNA ASP
KeywordsRIBOSOME / eukaryotic ribosome / homology modeling / de novo modeling / ribosomal proteins / novel ribosomal proteins
Function / homology
Function and homology information


: / cytoplasmic translational elongation / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity ...: / cytoplasmic translational elongation / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / 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) / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / G-protein alpha-subunit binding / ribosomal large subunit export from nucleus / protein kinase activator activity / 90S preribosome / ribonucleoprotein complex binding / protein-RNA complex assembly / regulation of translational fidelity / translational termination / maturation of LSU-rRNA / ribosomal 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) / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled cytosolic ribosome / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ribosomal protein L14, KOW motif / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ribosomal protein L14, KOW motif / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein S17e, conserved site / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L35Ae, conserved site / : / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S3, eukaryotic/archaeal / 60S ribosomal protein L35 / Ribosomal protein L6e / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein P1A / Large ribosomal subunit protein P2A / 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 eL33A / Large ribosomal subunit protein eL36A / 60S ribosomal protein L41-B / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / 40S ribosomal protein S4-B / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L18-A / 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 eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / Small ribosomal subunit protein eS24B / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / 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 / 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 / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / 40S ribosomal protein S24-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / 40S ribosomal protein S18-A / 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 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / 60S ribosomal protein L43-A / 60S ribosomal protein L1-B / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Large ribosomal subunit protein eL20 / 40S ribosomal protein S30-A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A / Large ribosomal subunit protein eL20
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsArmache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. ...Armache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. / Marquez, V. / Mielke, T. / Thomm, M. / Berninghausen, O. / Beatrix, B. / Soeding, J. / Westhof, E. / Wilson, D.N. / Beckmann, R.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2010
Title: Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter ...Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter Marquez / Thorsten Mielke / Michael Thomm / Otto Berninghausen / Birgitta Beatrix / Johannes Söding / Eric Westhof / Daniel N Wilson / Roland Beckmann /
Abstract: Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, ...Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2010
Title: Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter ...Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter Marquez / Thorsten Mielke / Michael Thomm / Otto Berninghausen / Birgitta Beatrix / Johannes Söding / Eric Westhof / Daniel N Wilson / Roland Beckmann /
Abstract: Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than ...Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution, together with a 6.1-Å map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3IZB, 3IZS, 3IZE, 3IZF
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 25, 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 ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type

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Assembly

Deposited unit
Aa: 40S ribosomal protein RACK1 (RACK1)
AA: 40S ribosomal protein rpS0 (S2p)
AB: 40S ribosomal protein rpS3 (S3p)
AD: 40S ribosomal protein rpS4 (S4e)
AC: 40S ribosomal protein rpS9 (S4p)
AE: 40S ribosomal protein rpS2 (S5p)
AG: 40S ribosomal protein rpS7 (S7e)
AF: 40S ribosomal protein rpS5 (S7p)
AH: 40S ribosomal protein rpS22 (S8p)
AI: 40S ribosomal protein rpS16 (S9p)
AJ: 40S ribosomal protein rpS20 (S10p)
AK: 40S ribosomal protein rpS14 (S11p)
AL: 40S ribosomal protein rpS23 (S12p)
AM: 40S ribosomal protein rpS18 (S13p)
AN: 40S ribosomal protein rpS29 (S14p)
AO: 40S ribosomal protein rpS13 (S15p)
AQ: 40S ribosomal protein rpS17 (S17e)
AP: 40S ribosomal protein rpS11 (S17p)
AR: 40S ribosomal protein rpS15 (S19p)
AS: 40S ribosomal protein rpS19 (S19e)
AT: 40S ribosomal protein rpS21 (S21e)
AV: 40S ribosomal protein rpS25 (S25e)
AW: 40S ribosomal protein rpS26 (S26e)
AX: 40S ribosomal protein rpS27 (S27e)
AY: 40S ribosomal protein rpS28 (S28e)
AZ: 40S ribosomal protein rpS30 (S30e)
Ab: Unknown 40S ribosomal protein XS1
Ac: Unknown 40S ribosomal protein XS2
AU: 40S ribosomal protein S24
BA: 60S ribosomal protein rpL1 (L1p)
BB: 60S ribosomal protein rpL2 (L2p)
BC: 60S ribosomal protein rpL3 (L3p)
BD: 60S ribosomal protein rpL4 (L4p)
BE: 60S ribosomal protein rpL11 (L5p)
BG: 60S ribosomal protein rpL6 (L6e)
BF: 60S ribosomal protein rpL9 (L6p)
BH: 60S ribosomal protein rpL8 (L7ae)
Bs: 60S acidic ribosomal protein rpP0 (L10P)
BJ: 60S ribosomal protein rpL12 (L11p)
BK: 60S ribosomal protein rpL16 (L13p)
BN: 60S ribosomal protein rpL14 (L14e)
BM: 60S ribosomal protein rpL23 (L14p)
BP: 60S ribosomal protein rpL15 (L15e)
BO: 60S ribosomal protein rpL28 (L15p)
BR: 60S ribosomal protein rpL18 (L18e)
BT: 60S ribosomal protein rpL19 (L19e)
BU: 60S ribosomal protein rpL21 (L21e)
BW: 60S ribosomal protein rpL22 (L22e)
BV: 60S ribosomal protein rpL17 (L22p)
BX: 60S ribosomal protein rpL25 (L23p)
BZ: 60S ribosomal protein rpL24 (L24e)
BY: 60S ribosomal protein rpL26 (L24p)
Ba: 60S ribosomal protein rpL27 (L27e)
Bd: 60S ribosomal protein rpL29 (L29e)
Bc: 60S ribosomal protein rpL35 (L29p)
Bf: 60S ribosomal protein rpL30 (L30e)
Be: 60S ribosomal protein rpL7 (L30p)
Bg: 60S ribosomal protein rpL31 (L31e)
Bh: 60S ribosomal protein pL32 (L32e)
Bi: 60S ribosomal protein rpL34 (L34e)
Bj: 60S ribosomal protein rpL33 (L35ae)
Bk: 60S ribosomal protein rpL36 (L36e)
Bm: 60S ribosomal protein rpL43 (L37ae)
Bl: 60S ribosomal protein rpL37 (L37e)
Bn: 60S ribosomal protein rpL38 (L38e)
Bo: 60S ribosomal protein rpL39 (L39e)
Bp: 60S ribosomal protein rpL40 (L40e)
Bq: 60S ribosomal protein rpL41 (L41e)
Br: 60S ribosomal protein rpL42 (L44e)
Bx: Unknown protein
By: Unknown protein
Bz: Unknown protein
Bt: 60S acidic ribosomal protein rpP11 (P1)
Bu: 60S acidic ribosomal protein rpP11 (P1)
Bv: 60S acidic ribosomal protein (P2)
Bw: 60S acidic ribosomal protein (P2)
BQ: 60S ribosomal protein rpL5 (L18p)
BL: 60S ribosomal protein rpL13 (L13e)
BS: 60S ribosomal protein rpL20 (L18ae)
BI: 60S ribosomal protein rpL10 (L10e)
CA: 18S rRNA
CB: P-SITE TRNA ASP
CC: MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')
DA: 25S rRNA
DB: 5.8S rRNA
DC: 5S rRNA


Theoretical massNumber of molelcules
Total (without water)3,104,13086
Polymers3,104,13086
Non-polymers00
Water00
1


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

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Components

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40S ribosomal protein ... , 27 types, 27 molecules AaAAABADACAEAGAFAHAIAJAKALAMANAOAQAPARASATAVAWAXAYAZAU

#1: Protein 40S ribosomal protein RACK1 (RACK1)


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
#2: Protein 40S ribosomal protein rpS0 (S2p)


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
#3: Protein 40S ribosomal protein rpS3 (S3p)


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
#4: Protein 40S ribosomal protein rpS4 (S4e)


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05753, UniProt: P0CX35*PLUS
#5: Protein 40S ribosomal protein rpS9 (S4p)


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
#6: Protein 40S ribosomal protein rpS2 (S5p)


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
#7: Protein 40S ribosomal protein rpS7 (S7e)


Mass: 12273.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#8: Protein 40S ribosomal protein rpS5 (S7p)


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
#9: Protein 40S ribosomal protein rpS22 (S8p)


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
#10: Protein 40S ribosomal protein rpS16 (S9p)


Mass: 15877.490 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
#11: Protein 40S ribosomal protein rpS20 (S10p)


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
#12: Protein 40S ribosomal protein rpS14 (S11p)


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
#13: Protein 40S ribosomal protein rpS23 (S12p)


Mass: 16073.896 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
#14: Protein 40S ribosomal protein rpS18 (S13p)


Mass: 17071.641 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
#15: Protein 40S ribosomal protein rpS29 (S14p)


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
#16: Protein 40S ribosomal protein rpS13 (S15p)


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
#17: Protein 40S ribosomal protein rpS17 (S17e)


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
#18: Protein 40S ribosomal protein rpS11 (S17p)


Mass: 17785.934 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
#19: Protein 40S ribosomal protein rpS15 (S19p)


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
#20: Protein 40S ribosomal protein rpS19 (S19e)


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
#21: Protein 40S ribosomal protein rpS21 (S21e)


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
#22: Protein 40S ribosomal protein rpS25 (S25e)


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
#23: Protein 40S ribosomal protein rpS26 (S26e)


Mass: 7932.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein 40S ribosomal protein rpS27 (S27e)


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
#25: Protein 40S ribosomal protein rpS28 (S28e)


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
#26: Protein 40S ribosomal protein rpS30 (S30e)


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12087, UniProt: P0CX33*PLUS
#29: Protein 40S ribosomal protein S24


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26782, UniProt: P0CX32*PLUS

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Unknown 40S ribosomal protein ... , 2 types, 2 molecules AbAc

#27: Protein/peptide Unknown 40S ribosomal protein XS1


Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#28: Protein/peptide Unknown 40S ribosomal protein XS2


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

+
60S ribosomal protein ... , 43 types, 43 molecules BABBBCBDBEBGBFBHBJBKBNBMBPBOBRBTBUBWBVBXBZBYBaBdBcBfBeBgBhBi...

#30: Protein 60S ribosomal protein rpL1 (L1p)


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
#31: Protein 60S ribosomal protein rpL2 (L2p)


Mass: 27463.574 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
#32: Protein 60S ribosomal protein rpL3 (L3p)


Mass: 43907.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#33: Protein 60S ribosomal protein rpL4 (L4p)


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
#34: Protein 60S ribosomal protein rpL11 (L5p)


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
#35: Protein 60S ribosomal protein rpL6 (L6e)


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
#36: Protein 60S ribosomal protein rpL9 (L6p)


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
#37: Protein 60S ribosomal protein rpL8 (L7ae)


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
#39: Protein 60S ribosomal protein rpL12 (L11p)


Mass: 17850.621 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
#40: Protein 60S ribosomal protein rpL16 (L13p)


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
#41: Protein 60S ribosomal protein rpL14 (L14e)


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: D6VXT1, UniProt: P36105*PLUS
#42: Protein 60S ribosomal protein rpL23 (L14p)


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
#43: Protein 60S ribosomal protein rpL15 (L15e)


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
#44: Protein 60S ribosomal protein rpL28 (L15p)


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
#45: Protein 60S ribosomal protein rpL18 (L18e)


Mass: 20609.252 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
#46: Protein 60S ribosomal protein rpL19 (L19e)


Mass: 21762.316 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
#47: Protein 60S ribosomal protein rpL21 (L21e)


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
#48: Protein 60S ribosomal protein rpL22 (L22e)


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
#49: Protein 60S ribosomal protein rpL17 (L22p)


Mass: 19007.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#50: Protein 60S ribosomal protein rpL25 (L23p)


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
#51: Protein 60S ribosomal protein rpL24 (L24e)


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
#52: Protein 60S ribosomal protein rpL26 (L24p)


Mass: 13837.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#53: Protein 60S ribosomal protein rpL27 (L27e)


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
#54: Protein 60S ribosomal protein rpL29 (L29e)


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
#55: Protein 60S ribosomal protein rpL35 (L29p)


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
#56: Protein 60S ribosomal protein rpL30 (L30e)


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
#57: Protein 60S ribosomal protein rpL7 (L30p)


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
#58: Protein 60S ribosomal protein rpL31 (L31e)


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
#59: Protein 60S ribosomal protein pL32 (L32e)


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
#60: Protein 60S ribosomal protein rpL34 (L34e)


Mass: 13343.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#61: Protein 60S ribosomal protein rpL33 (L35ae)


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
#62: Protein 60S ribosomal protein rpL36 (L36e)


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
#63: Protein 60S ribosomal protein rpL43 (L37ae)


Mass: 10112.952 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
#64: Protein 60S ribosomal protein rpL37 (L37e)


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
#65: Protein 60S ribosomal protein rpL38 (L38e)


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
#66: Protein 60S ribosomal protein rpL39 (L39e)


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
#67: Protein 60S ribosomal protein rpL40 (L40e)


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08
#68: Protein/peptide 60S ribosomal protein rpL41 (L41e)


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05746, UniProt: P0CX86*PLUS
#69: Protein 60S ribosomal protein rpL42 (L44e)


Mass: 12246.658 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
#74: Protein 60S ribosomal protein rpL5 (L18p)


Mass: 33792.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#75: Protein 60S ribosomal protein rpL13 (L13e)


Mass: 14485.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#76: Protein 60S ribosomal protein rpL20 (L18ae)


Mass: 20148.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q0JJA0, UniProt: Q943F3*PLUS
#77: Protein 60S ribosomal protein rpL10 (L10e)


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

-
60S acidic ribosomal protein ... , 3 types, 5 molecules BsBtBuBvBw

#38: Protein 60S acidic ribosomal protein rpP0 (L10P)


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
#72: Protein 60S acidic ribosomal protein rpP11 (P1)


Mass: 10928.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05318
#73: Protein 60S acidic ribosomal protein (P2)


Mass: 10752.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05319

-
Protein/peptide , 2 types, 3 molecules BxByBz

#70: Protein/peptide Unknown protein


Mass: 1805.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#71: Protein/peptide Unknown protein


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
RNA chain , 6 types, 6 molecules CACBCCDADBDC

#78: RNA chain 18S rRNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1
#79: RNA chain P-SITE TRNA ASP


Mass: 24135.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: M25599.1
#80: RNA chain MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')


Mass: 3498.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#81: RNA chain 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1
#82: RNA chain 5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1
#83: RNA chain 5S rRNA


Mass: 37947.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: U53879.1

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Saccharomyces cerevisiae translating 80S ribosome / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.8 Å / Num. of particles: 20400 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms28040 0 0 0 28040

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