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- PDB-5mc6: Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex fro... -

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Entry
Database: PDB / ID: 5mc6
TitleCryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 40
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • A-site tRNA
  • Antiviral helicase SKI2
  • Antiviral protein SKI8Antiviral drug
  • Eukaryotic translation initiation factor 5A-1
  • Guanine nucleotide-binding protein subunit beta-like protein
  • P-site tRNA
  • Superkiller protein 3
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
  • mRNAMessenger RNA
  • uL1
KeywordsRIBOSOME / cryo-EM / ribosome / RNA / helicase
Function / homologyRibosomal protein S17e-like superfamily / Ribosomal protein L16p/L10e / 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 L3 ...Ribosomal protein S17e-like superfamily / Ribosomal protein L16p/L10e / 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 L3 / Ribosomal protein L5 / Ribosomal protein L23 / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Ribosomal protein S14p/S29e / Ubiquitin family / WD domain, G-beta repeat / Ribosomal protein L14p/L23e / 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 / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein L22e superfamily / Ribosomal protein S6e / Ribosomal protein S24e / Ribosomal protein L19e / Ribosomal protein S7e / 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 S19e / Ribosomal protein S11 / Ribosomal L40e family / Ribosomal S3Ae family / 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 L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein S13/S18 / Ribosomal protein S26e superfamily / Ribosomal protein L7A/L8 superfamily / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Ribosomal protein L31e domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / 60S ribosomal protein L4, C-terminal domain / rRNA-processing arch 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 S2, flavodoxin-like domain superfamily / 50S ribosomal protein L30e-like / 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 / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsSchmidt, C. / Kowalinski, E. / Shanmuganathan, V. / Defenouillere, Q. / Braunger, K. / Heuer, A. / Pech, M. / Namane, A. / Berninghausen, O. / Fromont-Racine, M. / Jacquier, A. / Conti, E. / Becker, T. / Beckmann, R.
CitationJournal: Science / Year: 2016
Title: The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.
Authors: Christian Schmidt / Eva Kowalinski / Vivekanandan Shanmuganathan / Quentin Defenouillère / Katharina Braunger / André Heuer / Markus Pech / Abdelkader Namane / Otto Berninghausen / Micheline Fromont-Racine / Alain Jacquier / Elena Conti / Thomas Becker / Roland Beckmann
Abstract: Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski ...Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 9, 2016 / Release: Jan 18, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 18, 2017Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collection / Derived calculationsem_software / struct_conn_em_software.name

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Assembly

Deposited unit
2: 18S ribosomal RNA
A: 40S ribosomal protein S3
B: 40S ribosomal protein S5
C: 40S ribosomal protein S10-A
D: 40S ribosomal protein S12
E: 40S ribosomal protein S15
F: 40S ribosomal protein S16-A
G: 40S ribosomal protein S17-B
H: 40S ribosomal protein S18-A
I: 40S ribosomal protein S19-A
J: 40S ribosomal protein S20
K: 40S ribosomal protein S25-A
L: 40S ribosomal protein S28-B
M: 40S ribosomal protein S29-A
N: Ubiquitin-40S ribosomal protein S31
O: Guanine nucleotide-binding protein subunit beta-like protein
P: 40S ribosomal protein S0-A
Q: 40S ribosomal protein S1-A
R: 40S ribosomal protein S2
S: 40S ribosomal protein S4-A
T: 40S ribosomal protein S6-A
U: 40S ribosomal protein S7-A
V: 40S ribosomal protein S8-A
W: 40S ribosomal protein S9-A
X: 40S ribosomal protein S11-A
Y: 40S ribosomal protein S13
Z: 40S ribosomal protein S14-A
a: 40S ribosomal protein S21-A
b: 40S ribosomal protein S22-A
c: 40S ribosomal protein S23-A
d: 40S ribosomal protein S24-A
e: 40S ribosomal protein S26-A
f: 40S ribosomal protein S27-A
g: 40S ribosomal protein S30-A
l: mRNA
m: A-site tRNA
n: P-site tRNA
h: Antiviral helicase SKI2
i: Superkiller protein 3
j: Antiviral protein SKI8
k: Antiviral protein SKI8
AA: 60S ribosomal protein L8-A
AB: 60S ribosomal protein L23-A
AC: 60S ribosomal protein L36-A
AD: 60S ribosomal protein L9-A
AE: 60S ribosomal protein L24-A
AF: 60S ribosomal protein L37-A
AG: 60S ribosomal protein L11-A
AH: 60S ribosomal protein L25
AI: 60S ribosomal protein L38
AJ: 60S ribosomal protein L13-A
AK: 60S ribosomal protein L26-A
AL: 60S ribosomal protein L39
AM: 60S ribosomal protein L14-A
AN: 60S ribosomal protein L27-A
AO: Ubiquitin-60S ribosomal protein L40
AP: 60S ribosomal protein L42-A
AQ: 60S ribosomal protein L15-A
AR: 60S ribosomal protein L28
AS: 60S ribosomal protein L41-A
AT: 60S ribosomal protein L43-A
AU: 60S ribosomal protein L16-A
AV: 60S ribosomal protein L29
AW: 60S ribosomal protein L2-A
AX: 60S ribosomal protein L17-A
AY: 60S ribosomal protein L30
AZ: uL1
BA: 60S ribosomal protein L3
BB: 60S ribosomal protein L18-A
BC: 60S ribosomal protein L31-A
BD: 60S ribosomal protein L10
BE: 60S ribosomal protein L4-A
BF: 60S ribosomal protein L19-A
BG: 60S ribosomal protein L32
BH: 60S ribosomal protein L20-A
BI: 60S ribosomal protein L5
BJ: 60S ribosomal protein L21-A
BK: 60S ribosomal protein L33-A
BL: 60S ribosomal protein L22-A
BM: 60S ribosomal protein L6-A
BN: 60S ribosomal protein L34-A
BO: 60S ribosomal protein L7-A
BP: 60S ribosomal protein L35-A
BQ: 25S ribosomal RNA
BR: 5S ribosomal RNA
BS: 5.8S ribosomal RNA
BT: Eukaryotic translation initiation factor 5A-1


Theoretical massNumber of molelcules
Total (without water)3,599,38387
Polyers3,599,38387
Non-polymers00
Water0
1


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

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Components

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RNA chain , 7 types, 7 molecules 2lmnBQBRBS

#1: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: REF: 831416132
#35: RNA chain mRNA / Messenger RNA


Mass: 10494.894 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#36: RNA chain A-site tRNA


Mass: 24378.408 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#37: RNA chain P-site tRNA


Mass: 24815.684 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#83: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: REF: 831416132
#84: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1039024045
#85: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1102645687

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

#2: Protein/peptide 40S ribosomal protein S3 / / RP13 / YS3


Mass: 26542.789 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05750
#3: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26783
#4: Protein/peptide 40S ribosomal protein S10-A / Ribosome


Mass: 12757.445 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q08745
#5: Protein/peptide 40S ribosomal protein S12 /


Mass: 15488.631 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P48589
#6: Protein/peptide 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / YS21


Mass: 16031.907 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q01855
#7: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R


Mass: 15877.490 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX51
#8: Protein/peptide 40S ribosomal protein S17-B / Ribosome / RP51B


Mass: 15835.384 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P14127
#9: Protein/peptide 40S ribosomal protein S18-A / Ribosome


Mass: 17071.641 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX55
#10: Protein/peptide 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P07280
#11: Protein/peptide 40S ribosomal protein S20 /


Mass: 13929.044 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38701
#12: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / YS23


Mass: 12067.272 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q3E792
#13: Protein/peptide 40S ribosomal protein S28-B / Ribosome / S33 / YS27


Mass: 7578.822 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C0X0
#14: Protein/peptide 40S ribosomal protein S29-A / Ribosome / S36 / YS29


Mass: 6675.723 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P41057
#17: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A


Mass: 28051.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32905
#18: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A


Mass: 28798.467 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33442
#19: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 27490.826 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25443
#20: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX35
#21: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX37
#22: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26786
#23: Protein/peptide 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX39
#24: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O13516
#25: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX47
#26: Protein/peptide 40S ribosomal protein S13 / / S27a / YS15


Mass: 17059.945 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05756
#27: Protein/peptide 40S ribosomal protein S14-A / Ribosome / RP59A


Mass: 14562.655 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P06367
#28: Protein/peptide 40S ribosomal protein S21-A / Ribosome / S26 / YS25


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


Mass: 14650.062 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C0W1
#30: Protein/peptide 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX29
#31: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50


Mass: 15362.848 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX31
#32: Protein/peptide 40S ribosomal protein S26-A / Ribosome


Mass: 13538.922 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P39938
#33: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / YS20


Mass: 8893.391 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P35997
#34: Protein/peptide 40S ribosomal protein S30-A / Ribosome


Mass: 7137.541 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX33

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Protein/peptide , 8 types, 9 molecules NOhijkAOAZBT

#15: Protein/peptide Ubiquitin-40S ribosomal protein S31


Mass: 17254.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05759
#16: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34841.219 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38011
#38: Protein/peptide Antiviral helicase SKI2 / Superkiller protein 2


Mass: 146259.094 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P35207, RNA helicase
#39: Protein/peptide Superkiller protein 3


Mass: 163922.141 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P17883
#40: Protein/peptide Antiviral protein SKI8 / Antiviral drug / Superkiller protein 8


Mass: 44283.527 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02793
#55: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CH08
#66: Protein/peptide uL1


Mass: 17889.996 Da / Num. of mol.: 1
Details: Due to resolution, this protein was only built as a poly-ala model. The actual uL1 sequence can be ...Due to resolution, this protein was only built as a poly-ala model. The actual uL1 sequence can be obtained from Uniprot-ID P0CX43. We had the same situation with a previous deposition of our group (PDB-ID 5GAK).
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#86: Protein/peptide Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / Hypusine-containing protein HP2 / eIF-4D


Mass: 17222.406 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23301

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60S ribosomal protein ... , 40 types, 40 molecules AAABACADAEAFAGAHAIAJAKALAMANAPAQARASATAUAVAWAXAYBABBBCBDBEBF...

#41: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P17076
#42: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX41
#43: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05745
#44: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05738
#45: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04449
#46: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49166
#47: Protein/peptide 60S ribosomal protein L11-A / Ribosome / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C0W9
#48: Protein/peptide 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04456
#49: Protein/peptide 60S ribosomal protein L38 /


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49167
#50: Protein/peptide 60S ribosomal protein L13-A / Ribosome


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12690
#51: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05743
#52: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04650
#53: Protein/peptide 60S ribosomal protein L14-A / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P36105
#54: Protein/peptide 60S ribosomal protein L27-A / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C2H6
#56: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX27
#57: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05748
#58: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P02406
#59: Protein/peptide 60S ribosomal protein L41-A / Ribosome / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX86
#60: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX25
#61: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26784
#62: Protein/peptide 60S ribosomal protein L29 / / YL43


Mass: 6691.884 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05747
#63: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX45
#64: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05740
#65: Protein/peptide 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P14120
#67: Protein/peptide 60S ribosomal protein L3 / / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P14126
#68: Protein/peptide 60S ribosomal protein L18-A / Ribosome / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX49
#69: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C2H8
#70: Protein/peptide 60S ribosomal protein L10 / / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P41805
#71: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10664
#72: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX82
#73: Protein/peptide 60S ribosomal protein L32 /


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38061
#74: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX23
#75: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26321
#76: Protein/peptide 60S ribosomal protein L21-A / Ribosome


Mass: 18279.266 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02753
#77: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05744
#78: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05749
#79: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02326
#80: Protein/peptide 60S ribosomal protein L34-A / Ribosome


Mass: 13673.196 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P87262
#81: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05737
#82: Protein/peptide 60S ribosomal protein L35-A / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX84

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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: Native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae
Type: RIBOSOME
Entity ID: 1, 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, 83, 84, 85, 86, 87
Source: NATURAL
Molecular weightValue: 3.6 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
120 mMHEPESC8H18N2O4S1
2100 mMPotassium acetateKOAc1
310 mMMagnesium chlorideMgCl21
41 mMDTTC4H10O2S21
50.5 mMPMSFC7H7FO2S1
610 ug/mlCycloheximideC15H23NO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/PALLADIUM / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 kelvins

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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 / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.8 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 2
Image scansUsed frames/image: 1-10

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Processing

EM software
IDNameVersionCategoryDetails
1Gautomatch0.53particle selectionFor details, see http://www.mrc-lmb.cam.ac.uk/kzhang/
2EM-Toolsimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION1.4initial Euler assignment
12FREALIGN9.11classification
13FREALIGN9.113D reconstruction
14PHENIX1.10model refinementReal-space refinement
15REFMAC5.8model refinementReciprocal space refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 31503 / Symmetry type: POINT

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