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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 rRNA18S ribosomal RNA
  • 25S rRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')Messenger RNA
  • P-SITE TRNA ASP
KeywordsRIBOSOME / eukaryotic ribosome / homology modeling / de novo modeling / ribosomal proteins / novel ribosomal proteins
Function / homology60s Acidic ribosomal protein / Ribosomal protein L10 / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / Ribosomal protein L1p/L10e family ...60s Acidic ribosomal protein / Ribosomal protein L10 / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / Ribosomal protein L1p/L10e family / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein S13/S18 / Ribosomal protein S19e / Ribosomal protein S11 / Ribosomal protein S8 / WD domain, G-beta repeat / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L3 / Ribosomal L40e family / Ribosomal protein L21e / Ribosomal protein L23 / Ribosomal L22e protein family / Ribosomal protein L41 / Ribosomal protein S30 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L23, N-terminal domain / Ribosomal protein S5, C-terminal domain / S25 ribosomal protein / Ribosomal protein L14 / Ribosomal protein L37e / Ribosomal L38e protein family / Ribosomal L37ae protein family / Ribosomal L29e protein family / Ribosomal L27e protein family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L36e / Ribosomal protein S27 / Ribosomal protein L32 / S4 domain / Ribosomal protein S24e / Ribosomal protein L19e / Ribosomal protein S21e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L35Ae / Ribosomal protein L24e / Ribosomal protein S28e / Ribosomal protein L34e / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L5 / Ribosomal protein S14p/S29e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19, eukaryotic / Ribosomal protein L11/L12, N-terminal domain superfamily / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 60S acidic ribosomal protein P0 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L12 family / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L40e superfamily / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.8 Å resolution
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.
CitationJournal: 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 Marquez / Thorsten Mielke / Michael Thomm / Otto Berninghausen / Birgitta Beatrix / Johannes Söding / Eric Westhof / Daniel N Wilson / Roland Beckmann
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 AaAAABADACAEAGAFAHAIAJAKALAMANAOAQAPARASATAVAWAXAYAZAU

#1: Protein/peptide 40S ribosomal protein RACK1 (RACK1) / Ribosome


Mass: 34841.219 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38011
#2: Protein/peptide 40S ribosomal protein rpS0 (S2p) / Ribosome


Mass: 28051.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32905
#3: Protein/peptide 40S ribosomal protein rpS3 (S3p) / Ribosome


Mass: 26542.789 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05750
#4: Protein/peptide 40S ribosomal protein rpS4 (S4e) / Ribosome


Mass: 29469.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05753, UniProt: P0CX36*PLUS
#5: Protein/peptide 40S ribosomal protein rpS9 (S4p) / Ribosome


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: O13516
#6: Protein/peptide 40S ribosomal protein rpS2 (S5p) / Ribosome


Mass: 27490.826 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25443
#7: Protein/peptide 40S ribosomal protein rpS7 (S7e) / Ribosome


Mass: 12273.120 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#8: Protein/peptide 40S ribosomal protein rpS5 (S7p) / Ribosome


Mass: 25072.600 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26783
#9: Protein/peptide 40S ribosomal protein rpS22 (S8p) / Ribosome


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W1
#10: Protein/peptide 40S ribosomal protein rpS16 (S9p) / Ribosome


Mass: 15877.490 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40213, UniProt: P0CX52*PLUS
#11: Protein/peptide 40S ribosomal protein rpS20 (S10p) / Ribosome


Mass: 13929.044 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38701
#12: Protein/peptide 40S ribosomal protein rpS14 (S11p) / Ribosome


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P06367
#13: Protein/peptide 40S ribosomal protein rpS23 (S12p) / Ribosome


Mass: 16073.896 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32827, UniProt: P0CX29*PLUS
#14: Protein/peptide 40S ribosomal protein rpS18 (S13p) / Ribosome


Mass: 17071.641 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35271, UniProt: P0CX56*PLUS
#15: Protein/peptide 40S ribosomal protein rpS29 (S14p) / Ribosome


Mass: 6675.723 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41057
#16: Protein/peptide 40S ribosomal protein rpS13 (S15p) / Ribosome


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05756
#17: Protein/peptide 40S ribosomal protein rpS17 (S17e) / Ribosome


Mass: 15820.413 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02407
#18: Protein/peptide 40S ribosomal protein rpS11 (S17p) / Ribosome


Mass: 17785.934 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26781, UniProt: P0CX48*PLUS
#19: Protein/peptide 40S ribosomal protein rpS15 (S19p) / Ribosome


Mass: 16031.907 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q01855
#20: Protein/peptide 40S ribosomal protein rpS19 (S19e) / Ribosome


Mass: 15942.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P07280
#21: Protein/peptide 40S ribosomal protein rpS21 (S21e) / Ribosome


Mass: 9758.829 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0V8
#22: Protein/peptide 40S ribosomal protein rpS25 (S25e) / Ribosome


Mass: 12067.272 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E792
#23: Protein/peptide 40S ribosomal protein rpS26 (S26e) / Ribosome


Mass: 7932.770 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#24: Protein/peptide 40S ribosomal protein rpS27 (S27e) / Ribosome


Mass: 8893.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35997
#25: Protein/peptide 40S ribosomal protein rpS28 (S28e) / Ribosome


Mass: 7605.847 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E7X9
#26: Protein/peptide 40S ribosomal protein rpS30 (S30e) / Ribosome


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


Mass: 15362.848 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26782, UniProt: P0CX31*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: (natural) Saccharomyces cerevisiae (baker's yeast)
#28: Protein/peptide Unknown 40S ribosomal protein XS2


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

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

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


Mass: 24524.799 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53030, UniProt: P0CX44*PLUS
#31: Protein/peptide 60S ribosomal protein rpL2 (L2p) / Ribosome


Mass: 27463.574 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05736, UniProt: P0CX46*PLUS
#32: Protein/peptide 60S ribosomal protein rpL3 (L3p) / Ribosome


Mass: 43907.844 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#33: Protein/peptide 60S ribosomal protein rpL4 (L4p) / Ribosome


Mass: 39159.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#34: Protein/peptide 60S ribosomal protein rpL11 (L5p) / Ribosome


Mass: 19755.691 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W9
#35: Protein/peptide 60S ribosomal protein rpL6 (L6e) / Ribosome


Mass: 20000.564 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#36: Protein/peptide 60S ribosomal protein rpL9 (L6p) / Ribosome


Mass: 21605.061 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#37: Protein/peptide 60S ribosomal protein rpL8 (L7ae) / Ribosome


Mass: 28175.820 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#39: Protein/peptide 60S ribosomal protein rpL12 (L11p) / Ribosome


Mass: 17850.621 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17079, UniProt: P0CX54*PLUS
#40: Protein/peptide 60S ribosomal protein rpL16 (L13p) / Ribosome


Mass: 22247.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#41: Protein/peptide 60S ribosomal protein rpL14 (L14e) / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: D6VXT1, UniProt: P36105*PLUS
#42: Protein/peptide 60S ribosomal protein rpL23 (L14p) / Ribosome


Mass: 14493.950 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04451, UniProt: P0CX42*PLUS
#43: Protein/peptide 60S ribosomal protein rpL15 (L15e) / Ribosome


Mass: 24482.357 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#44: Protein/peptide 60S ribosomal protein rpL28 (L15p) / Ribosome


Mass: 16761.666 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#45: Protein/peptide 60S ribosomal protein rpL18 (L18e) / Ribosome


Mass: 20609.252 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P07279, UniProt: P0CX50*PLUS
#46: Protein/peptide 60S ribosomal protein rpL19 (L19e) / Ribosome


Mass: 21762.316 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05735, UniProt: P0CX82*PLUS
#47: Protein/peptide 60S ribosomal protein rpL21 (L21e) / Ribosome


Mass: 18279.266 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#48: Protein/peptide 60S ribosomal protein rpL22 (L22e) / Ribosome


Mass: 13711.359 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#49: Protein/peptide 60S ribosomal protein rpL17 (L22p) / Ribosome


Mass: 19007.621 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#50: Protein/peptide 60S ribosomal protein rpL25 (L23p) / Ribosome


Mass: 15787.612 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#51: Protein/peptide 60S ribosomal protein rpL24 (L24e) / Ribosome


Mass: 17661.717 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449
#52: Protein/peptide 60S ribosomal protein rpL26 (L24p) / Ribosome


Mass: 13837.280 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#53: Protein/peptide 60S ribosomal protein rpL27 (L27e) / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#54: Protein/peptide 60S ribosomal protein rpL29 (L29e) / Ribosome


Mass: 6691.884 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05747
#55: Protein/peptide 60S ribosomal protein rpL35 (L29p) / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39741, UniProt: P0CX84*PLUS
#56: Protein/peptide 60S ribosomal protein rpL30 (L30e) / Ribosome


Mass: 11430.364 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#57: Protein/peptide 60S ribosomal protein rpL7 (L30p) / Ribosome


Mass: 27686.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#58: Protein/peptide 60S ribosomal protein rpL31 (L31e) / Ribosome


Mass: 12980.158 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#59: Protein/peptide 60S ribosomal protein pL32 (L32e) / Ribosome


Mass: 14809.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#60: Protein/peptide 60S ribosomal protein rpL34 (L34e) / Ribosome


Mass: 13343.759 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#61: Protein/peptide 60S ribosomal protein rpL33 (L35ae) / Ribosome


Mass: 12177.130 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#62: Protein/peptide 60S ribosomal protein rpL36 (L36e) / Ribosome


Mass: 11151.259 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#63: Protein/peptide 60S ribosomal protein rpL43 (L37ae) / Ribosome


Mass: 10112.952 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49631, UniProt: P0CX25*PLUS
#64: Protein/peptide 60S ribosomal protein rpL37 (L37e) / Ribosome


Mass: 9877.395 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#65: Protein/peptide 60S ribosomal protein rpL38 (L38e) / Ribosome


Mass: 8845.561 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#66: Protein/peptide 60S ribosomal protein rpL39 (L39e) / Ribosome


Mass: 6358.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#67: Protein/peptide 60S ribosomal protein rpL40 (L40e) / Ribosome


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


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05746, UniProt: P0CX87*PLUS
#69: Protein/peptide 60S ribosomal protein rpL42 (L44e) / Ribosome


Mass: 12246.658 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02405, UniProt: P0CX27*PLUS
#74: Protein/peptide 60S ribosomal protein rpL5 (L18p) / Ribosome


Mass: 33792.844 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#75: Protein/peptide 60S ribosomal protein rpL13 (L13e) / Ribosome


Mass: 14485.838 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#76: Protein/peptide 60S ribosomal protein rpL20 (L18ae) / Ribosome


Mass: 20148.668 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q0JJA0, UniProt: Q943F3*PLUS
#77: Protein/peptide 60S ribosomal protein rpL10 (L10e) / Ribosome


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

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

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


Mass: 33749.121 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05317
#72: Protein/peptide 60S acidic ribosomal protein rpP11 (P1)


Mass: 10928.809 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05318
#73: Protein/peptide 60S acidic ribosomal protein (P2)


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

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Protein/peptide , 2 types, 3 molecules BxByBz

#70: Protein/peptide Unknown protein


Mass: 1805.216 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#71: Protein/peptide Unknown protein


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

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RNA chain , 6 types, 6 molecules CACBCCDADBDC

#78: RNA chain 18S rRNA / 18S ribosomal RNA


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


Mass: 24135.262 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker'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') / Messenger RNA


Mass: 3498.178 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#81: RNA chain 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: U53879.1
#82: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: U53879.1
#83: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37947.492 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / 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 reconstruction

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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 FIELDBright-field microscopy / 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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