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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
DescriptorRibosome
KeywordsRIBOSOME / eukaryotic ribosome / homology modeling / de novo modeling / ribosomal proteins / novel ribosomal proteins
Specimen sourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (8.8 Å resolution / Particle / Single particle)
AuthorsArmache, 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.
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 19748-19753

primary. Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 19748-19753 Yorodumi Papers
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
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

#1. Proc.Natl.Acad.Sci.USA, 2010, 107, 19754-19759 Yorodumi Papers
Localization of eukaryote-specific ribosomal proteins in a 5.5-A cryo-EM map of the 80S eukaryotic ribosome.
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. / Soding, J. / Westhof, E. / Wilson, D.N. / Beckmann, R.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2010 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Mar 25, 2015Structure modelOther

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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
Polyers3,104,13086
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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40S ribosomal protein ... , 27 types, 27 molecules AaAAABADACAEAGAFAHAI...

#1: Polypeptide(L)40S ribosomal protein RACK1 (RACK1)


Mass: 34841.219 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P38011

Cellular component

Molecular function

Biological process

  • G-protein coupled receptor signaling pathway (GO: 0007186)
  • invasive growth in response to glucose limitation (GO: 0001403)
  • negative regulation of glucose mediated signaling pathway (GO: 1902660)
  • negative regulation of translation (GO: 0017148)
  • negative regulation of translational frameshifting (GO: 2001125)
#2: Polypeptide(L)40S ribosomal protein rpS0 (S2p)


Mass: 28051.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P32905

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • 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) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • ribosomal small subunit assembly (GO: 0000028)
  • rRNA export from nucleus (GO: 0006407)
#3: Polypeptide(L)40S ribosomal protein rpS3 (S3p)


Mass: 26542.789 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05750

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)40S ribosomal protein rpS4 (S4e)


Mass: 29469.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05753

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)40S ribosomal protein rpS9 (S4p)


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: O13516

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • positive regulation of translational fidelity (GO: 0045903)
  • rRNA methylation (GO: 0031167)
#6: Polypeptide(L)40S ribosomal protein rpS2 (S5p)


Mass: 27490.826 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P25443

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)40S ribosomal protein rpS7 (S7e)


Mass: 12273.120 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#8: Polypeptide(L)40S ribosomal protein rpS5 (S7p)


Mass: 25072.600 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26783

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)40S ribosomal protein rpS22 (S8p)


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C0W1

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)40S ribosomal protein rpS16 (S9p)


Mass: 15877.490 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P40213

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)40S ribosomal protein rpS20 (S10p)


Mass: 13929.044 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P38701

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#12: Polypeptide(L)40S ribosomal protein rpS14 (S11p)


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P06367

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)40S ribosomal protein rpS23 (S12p)


Mass: 16073.896 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P32827

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • regulation of translational fidelity (GO: 0006450)
  • translation (GO: 0006412)
#14: Polypeptide(L)40S ribosomal protein rpS18 (S13p)


Mass: 17071.641 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P35271

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • 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) (GO: 0000447)
  • rRNA export from nucleus (GO: 0006407)
  • translation (GO: 0006412)
#15: Polypeptide(L)40S ribosomal protein rpS29 (S14p)


Mass: 6675.723 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P41057

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)40S ribosomal protein rpS13 (S15p)


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05756

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)40S ribosomal protein rpS17 (S17e)


Mass: 15820.413 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P02407

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)40S ribosomal protein rpS11 (S17p)


Mass: 17785.934 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26781

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)40S ribosomal protein rpS15 (S19p)


Mass: 16031.907 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q01855

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)40S ribosomal protein rpS19 (S19e)


Mass: 15942.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P07280

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)40S ribosomal protein rpS21 (S21e)


Mass: 9758.829 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C0V8

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • 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) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
#22: Polypeptide(L)40S ribosomal protein rpS25 (S25e)


Mass: 12067.272 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q3E792

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)40S ribosomal protein rpS26 (S26e)


Mass: 7932.770 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#24: Polypeptide(L)40S ribosomal protein rpS27 (S27e)


Mass: 8893.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P35997

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)40S ribosomal protein rpS28 (S28e)


Mass: 7605.847 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q3E7X9

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)40S ribosomal protein rpS30 (S30e)


Mass: 7137.541 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q12087

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)40S ribosomal protein S24


Mass: 15362.848 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26782

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)

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

#27: Polypeptide(L)Unknown 40S ribosomal protein XS1


Mass: 3166.895 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#28: Polypeptide(L)Unknown 40S ribosomal protein XS2


Mass: 2230.741 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae

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60S ribosomal protein ... , 43 types, 43 molecules BABBBCBDBEBGBFBHBJBK...

#30: Polypeptide(L)60S ribosomal protein rpL1 (L1p)


Mass: 24524.799 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P53030

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)60S ribosomal protein rpL2 (L2p)


Mass: 27463.574 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05736

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)60S ribosomal protein rpL3 (L3p)


Mass: 43907.844 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P14126

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)60S ribosomal protein rpL4 (L4p)


Mass: 39159.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P10664

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)60S ribosomal protein rpL11 (L5p)


Mass: 19755.691 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C0W9

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)60S ribosomal protein rpL6 (L6e)


Mass: 20000.564 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q02326

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)60S ribosomal protein rpL9 (L6p)


Mass: 21605.061 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05738

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein rpL8 (L7ae)


Mass: 28175.820 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P17076

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)60S ribosomal protein rpL12 (L11p)


Mass: 17850.621 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P17079

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)60S ribosomal protein rpL16 (L13p)


Mass: 22247.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26784

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein rpL14 (L14e)


Mass: 15195.066 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: D6VXT1

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)60S ribosomal protein rpL23 (L14p)


Mass: 14493.950 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P04451

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein rpL15 (L15e)


Mass: 24482.357 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05748

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein rpL28 (L15p)


Mass: 16761.666 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P02406

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein rpL18 (L18e)


Mass: 20609.252 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P07279

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)60S ribosomal protein rpL19 (L19e)


Mass: 21762.316 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05735

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)60S ribosomal protein rpL21 (L21e)


Mass: 18279.266 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q02753

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)60S ribosomal protein rpL22 (L22e)


Mass: 13711.359 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05749

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)60S ribosomal protein rpL17 (L22p)


Mass: 19007.621 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05740

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
#50: Polypeptide(L)60S ribosomal protein rpL25 (L23p)


Mass: 15787.612 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P04456

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)60S ribosomal protein rpL24 (L24e)


Mass: 17661.717 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P04449

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)60S ribosomal protein rpL26 (L24p)


Mass: 13837.280 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05743

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)60S ribosomal protein rpL27 (L27e)


Mass: 15568.360 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C2H6

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)60S ribosomal protein rpL29 (L29e)


Mass: 6691.884 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05747

Cellular component

Molecular function

Biological process

#55: Polypeptide(L)60S ribosomal protein rpL35 (L29p)


Mass: 13942.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P39741

Cellular component

Molecular function

Biological process

#56: Polypeptide(L)60S ribosomal protein rpL30 (L30e)


Mass: 11430.364 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P14120

Cellular component

Molecular function

Biological process

#57: Polypeptide(L)60S ribosomal protein rpL7 (L30p)


Mass: 27686.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05737

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of LSU-rRNA (GO: 0000470)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • ribosomal large subunit biogenesis (GO: 0042273)
#58: Polypeptide(L)60S ribosomal protein rpL31 (L31e)


Mass: 12980.158 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

#59: Polypeptide(L)60S ribosomal protein pL32 (L32e)


Mass: 14809.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P38061

Cellular component

Molecular function

Biological process

#60: Polypeptide(L)60S ribosomal protein rpL34 (L34e)


Mass: 13343.759 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P87262

Cellular component

Molecular function

Biological process

#61: Polypeptide(L)60S ribosomal protein rpL33 (L35ae)


Mass: 12177.130 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05744

Cellular component

Molecular function

Biological process

#62: Polypeptide(L)60S ribosomal protein rpL36 (L36e)


Mass: 11151.259 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05745

Cellular component

Molecular function

Biological process

#63: Polypeptide(L)60S ribosomal protein rpL43 (L37ae)


Mass: 10112.952 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P49631

Cellular component

Molecular function

Biological process

#64: Polypeptide(L)60S ribosomal protein rpL37 (L37e)


Mass: 9877.395 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P49166

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
  • translation (GO: 0006412)
#65: Polypeptide(L)60S ribosomal protein rpL38 (L38e)


Mass: 8845.561 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P49167

Cellular component

Molecular function

Biological process

#66: Polypeptide(L)60S ribosomal protein rpL39 (L39e)


Mass: 6358.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P04650

Cellular component

Molecular function

Biological process

#67: Polypeptide(L)60S ribosomal protein rpL40 (L40e)


Mass: 6032.321 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CH08

Cellular component

Molecular function

Biological process

#68: Polypeptide(L)60S ribosomal protein rpL41 (L41e)


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05746

Cellular component

Molecular function

Biological process

#69: Polypeptide(L)60S ribosomal protein rpL42 (L44e)


Mass: 12246.658 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P02405

Cellular component

Molecular function

Biological process

#74: Polypeptide(L)60S ribosomal protein rpL5 (L18p)


Mass: 33792.844 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26321

Cellular component

Molecular function

Biological process

#75: Polypeptide(L)60S ribosomal protein rpL13 (L13e)


Mass: 14485.838 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#76: Polypeptide(L)60S ribosomal protein rpL20 (L18ae)


Mass: 20148.668 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q0JJA0

Cellular component

Molecular function

Biological process

#77: Polypeptide(L)60S ribosomal protein rpL10 (L10e)


Mass: 25410.465 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P41805

Cellular component

Molecular function

Biological process

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

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


Mass: 33749.121 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05317

Cellular component

Molecular function

Biological process

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


Mass: 10928.809 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05318

Cellular component

Molecular function

Biological process

#73: Polypeptide(L)60S acidic ribosomal protein (P2)


Mass: 10752.715 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05319

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 3 molecules BxByBz

#70: Polypeptide(L)Unknown protein


Mass: 1805.216 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae
#71: Polypeptide(L)Unknown protein


Mass: 1294.587 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae

+
RNA chain , 6 types, 6 molecules CACBCCDADBDC

#78: RNA chain18S rRNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: U53879.1
#79: RNA chainP-SITE TRNA ASP


Mass: 24135.262 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: M25599.1
#80: RNA chainMRNA, 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: (natural) Saccharomyces cerevisiae
#81: RNA chain25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: U53879.1
#82: RNA chain5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: U53879.1
#83: RNA chain5S rRNA


Mass: 37947.492 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: U53879.1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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

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Electron microscopy imaging

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

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Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.8 Å / Number of particles: 20400 / Symmetry type: POINT
Number of atoms included #LASTProtein: 28040 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 28040

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