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- PDB-6gq1: Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA... -

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Entry
Database: PDB / ID: 6gq1
TitleCryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin)
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 41
  • 18S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Elongation factor 2EEF2
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Messenger RNA
  • Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
  • Transfer RNA - Phe
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Eukaryotic 80S riboosme / mRNA-tRNA translocation / diphthamide / ribosome
Function / homologyRibosomal protein L21 superfamily / Ubiquitin family / 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 L21 superfamily / Ubiquitin family / 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 protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / WD domain, G-beta repeat / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Elongation factor Tu GTP binding domain / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / S27a-like superfamily / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein L34Ae superfamily / Ribosomal L40e family / Ribosomal protein S21e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L35Ae / Ribosomal protein L24e / Ribosomal protein S8e / Ribosomal protein S28e / Ribosomal protein L34e / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal S3Ae family / Ribosomal protein S11 / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / Elongation factor G C-terminus / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein L10 / Ribosomal protein S13/S18 / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / Ribosomal protein L19e / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Tr-type G domain, conserved site / 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 S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S11, N-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L22e superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L7A/L8 superfamily
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsPellegrino, S. / Demeshkina, N. / Mancera-Martinez, E. / Melnikov, S. / Simonetti, A. / Myasnikov, A. / Yusupov, M. / Yusupova, G. / Hashem, Y.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance.
Authors: Simone Pellegrino / Natalia Demeshkina / Eder Mancera-Martinez / Sergey Melnikov / Angelita Simonetti / Alexander Myasnikov / Marat Yusupov / Gulnara Yusupova / Yaser Hashem
Abstract: One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a ...One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 7, 2018 / Release: Jul 11, 2018

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Assembly

Deposited unit
1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
3: 5.8S ribosomal RNA
4: 5S ribosomal RNA
P0: 60S acidic ribosomal protein P0
P2: 60S ribosomal protein L12-A
A: 60S ribosomal protein L2-A
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
H: 60S ribosomal protein L9-A
I: 60S ribosomal protein L10
J: 60S ribosomal protein L11-B
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
T: 60S ribosomal protein L21-A
U: 60S ribosomal protein L22-A
V: 60S ribosomal protein L23-A
W: 60S ribosomal protein L24-A
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
b: 60S ribosomal protein L29
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
m: Ubiquitin-60S ribosomal protein L40
n: 60S ribosomal protein L41-B
o: 60S ribosomal protein L42-A
p: 60S ribosomal protein L43-A
2: 18S ribosomal RNA
q: 40S ribosomal protein S0-A
r: 40S ribosomal protein S1-A
s: 40S ribosomal protein S2
t: 40S ribosomal protein S3
u: 40S ribosomal protein S4-A
v: 40S ribosomal protein S5
w: 40S ribosomal protein S6-A
x: 40S ribosomal protein S7-A
y: 40S ribosomal protein S8-A
z: 40S ribosomal protein S9-A
AA: 40S ribosomal protein S10-A
AB: 40S ribosomal protein S11-A
AC: 40S ribosomal protein S12
AD: 40S ribosomal protein S13
AE: 40S ribosomal protein S14-B
AF: 40S ribosomal protein S15
AG: 40S ribosomal protein S16-A
AH: 40S ribosomal protein S17-B
AI: 40S ribosomal protein S18-A
AJ: 40S ribosomal protein S19-A
AK: 40S ribosomal protein S20
AL: 40S ribosomal protein S21-A
AM: 40S ribosomal protein S22-A
AN: 40S ribosomal protein S23-A
AO: 40S ribosomal protein S24-A
AP: 40S ribosomal protein S25-A
AQ: 40S ribosomal protein S26-B
AR: 40S ribosomal protein S27-A
AS: 40S ribosomal protein S28-A
AT: 40S ribosomal protein S29-A
AU: 40S ribosomal protein S30-A
AV: Guanine nucleotide-binding protein subunit beta-like protein
AW: Ubiquitin-40S ribosomal protein S31
AX: Transfer RNA - Phe
AY: Messenger RNA
AZ: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,169,72793
Polyers3,168,18883
Non-polymers1,53910
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 6 molecules 1342AXAY

#1: RNA chain Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: REF: 831416132
#2: RNA chain 5.8S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1329886537
#3: RNA chain 5S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1358044889
#47: RNA chain 18S ribosomal RNA /


Mass: 578820.375 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1329886537
#81: RNA chain Transfer RNA - Phe


Mass: 24518.570 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 176419
#82: RNA chain Messenger RNA /


Mass: 2449.465 Da / Num. of mol.: 1
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Protein/peptide , 5 types, 5 molecules P0mAVAWAZ

#4: Protein/peptide 60S acidic ribosomal protein P0 / A0 / L10e / Large ribosomal subunit protein uL10


Mass: 20929.145 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05317
#43: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CH08
#79: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34710.023 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38011
#80: Protein/peptide Ubiquitin-40S ribosomal protein S31


Mass: 4148.841 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05759
#83: Protein/peptide Elongation factor 2 / EEF2 / EF-2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase / Translation elongation factor 2


Mass: 93318.992 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32324

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60S ribosomal protein ... , 41 types, 41 molecules P2ABCDEFGHIJLMNOPQRSTUVWXYZabcd...

#5: Protein/peptide 60S ribosomal protein L12-A / Ribosome / L15 / Large ribosomal subunit protein uL11-A / YL23


Mass: 10347.016 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX53
#6: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27217.289 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX45
#7: Protein/peptide 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P14126
#8: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10664
#9: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33633.633 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26321
#10: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02326
#11: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 25240.377 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05737
#12: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P17076
#13: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05738
#14: Protein/peptide 60S ribosomal protein L10 / / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25279.271 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P41805
#15: Protein/peptide 60S ribosomal protein L11-B / Ribosome / L16 / Large ribosomal subunit protein uL5-B / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q3E757
#16: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 21885.234 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12690
#17: Protein/peptide 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 14976.794 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P36105
#18: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05748
#19: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26784
#20: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20458.322 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05740
#21: Protein/peptide 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#22: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#23: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#24: Protein/peptide 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18148.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#25: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05749
#26: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14362.755 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#27: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 7384.708 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04449
#28: Protein/peptide 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#29: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14134.588 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05743
#30: Protein/peptide 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15437.166 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#31: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#32: Protein/peptide 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43


Mass: 6560.688 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05747
#33: Protein/peptide 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 10558.344 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#34: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#35: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14478.054 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#36: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#37: Protein/peptide 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 12608.831 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P87262
#38: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13811.444 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#39: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11020.063 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05745
#40: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#41: Protein/peptide 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8714.363 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#42: Protein/peptide 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6227.444 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#44: Protein/peptide 60S ribosomal protein L41-B / Ribosome / L47 / Large ribosomal subunit protein eL41-B / YL41


Mass: 3354.243 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX87
#45: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#46: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 9981.756 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX25

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40S ribosomal protein ... , 31 types, 31 molecules qrstuvwxyzAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU

#48: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 22811.074 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32905
#49: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 24312.199 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33442
#50: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 23212.979 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25443
#51: Protein/peptide 40S ribosomal protein S3 / / RP13 / Small ribosomal subunit protein uS3 / YS3


Mass: 24702.791 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05750
#52: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29338.133 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#53: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 22908.338 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#54: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 25581.721 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#55: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21000.492 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#56: Protein/peptide 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22406.609 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#57: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 21210.662 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#58: Protein/peptide 40S ribosomal protein S10-A / Ribosome / Small ribosomal subunit protein eS10-A


Mass: 12757.445 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08745
#59: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17378.383 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#60: Protein/peptide 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 13327.331 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48589
#61: Protein/peptide 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 16928.748 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#62: Protein/peptide 40S ribosomal protein S14-B / Ribosome / RP59B / Small ribosomal subunit protein uS11-B


Mass: 13446.426 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39516
#63: Protein/peptide 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 14155.720 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01855
#64: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15659.216 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#65: Protein/peptide 40S ribosomal protein S17-B / Ribosome / RP51B / Small ribosomal subunit protein eS17-B


Mass: 14268.545 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14127
#66: Protein/peptide 40S ribosomal protein S18-A / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 16940.443 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#67: Protein/peptide 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07280
#68: Protein/peptide 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 12190.175 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38701
#69: Protein/peptide 40S ribosomal protein S21-A / Ribosome / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0V8
#70: Protein/peptide 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#71: Protein/peptide 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 15942.699 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#72: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15231.650 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#73: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 8001.377 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E792
#74: Protein/peptide 40S ribosomal protein S26-B / Ribosome / Small ribosomal subunit protein eS26-B


Mass: 11022.989 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39939
#75: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8762.195 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#76: Protein/peptide 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7116.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9
#77: Protein/peptide 40S ribosomal protein S29-A / Ribosome / S36 / Small ribosomal subunit protein uS14-A / YS29


Mass: 6335.303 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41057
#78: Protein/peptide 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


Mass: 6779.086 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX33

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Non-polymers , 3 types, 10 molecules

#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#85: Chemical ChemComp-SO1 / [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID / SORDARIN


Mass: 494.618 Da / Num. of mol.: 1 / Formula: C27H42O8
#86: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Formula: C11H18N5O13P3 / Comment: GMP-PCP (energy-carrying molecule analogue) *YM

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Experimental details

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Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
180S ribosome in complex with mRNA, tRNA and eEF2 in presence of non-hydrolizable GTP (GMPPCP) and anti-fungal drug (sordarin)RIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 830MULTIPLE SOURCES
280S ribosomeCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 831NATURAL
3RNACOMPLEX821RECOMBINANT
Molecular weightValue: 3.4 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
23559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.FormulaBuffer ID
110 mMHepes-KOH1
25 mMMg(OAc)21
340 mMKOAc1
410 mMNH4Cl1
51 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: blot force 4, blot waiting time 30 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 189700 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL

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