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

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Database: PDB / ID: 5mc6
TitleCryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae
Descriptor40S ribosomal protein S3, 40S ribosomal protein S5, 40S ribosomal protein S10-A, 40S ribosomal protein S12, 40S ribosomal protein S15, 40S ribosomal protein S16-A, 40S ribosomal protein S17-B, 40S ribosomal protein S18-A, 40S ribosomal protein S19-A, 40S ribosomal protein S20, 40S ribosomal protein S25-A, 40S ribosomal protein S28-B, 40S ribosomal protein S29-A, Ubiquitin-40S ribosomal protein S31, Guanine nucleotide-binding protein subunit beta-like protein, 40S ribosomal protein S0-A, 40S ribosomal protein S1-A, 40S ribosomal protein S2, 40S ribosomal protein S4-A, 40S ribosomal protein S6-A, 40S ribosomal protein S7-A, 40S ribosomal protein S8-A, 40S ribosomal protein S9-A, 40S ribosomal protein S11-A, 40S ribosomal protein S13, 40S ribosomal protein S14-A, 40S ribosomal protein S21-A, 40S ribosomal protein S22-A, 40S ribosomal protein S23-A, 40S ribosomal protein S24-A, 40S ribosomal protein S26-A, 40S ribosomal protein S27-A, 40S ribosomal protein S30-A, Antiviral helicase SKI2, Superkiller protein 3, Antiviral protein SKI8, 60S ribosomal protein L8-A, 60S ribosomal protein L23-A, 60S ribosomal protein L36-A, 60S ribosomal protein L9-A, 60S ribosomal protein L24-A, 60S ribosomal protein L37-A, 60S ribosomal protein L11-A, 60S ribosomal protein L25, 60S ribosomal protein L38, 60S ribosomal protein L13-A, 60S ribosomal protein L26-A, 60S ribosomal protein L39, 60S ribosomal protein L14-A, 60S ribosomal protein L27-A, Ubiquitin-60S ribosomal protein L40, 60S ribosomal protein L42-A, 60S ribosomal protein L15-A, 60S ribosomal protein L28, 60S ribosomal protein L41-A, 60S ribosomal protein L43-A, 60S ribosomal protein L16-A, 60S ribosomal protein L29, 60S ribosomal protein L2-A, 60S ribosomal protein L17-A, 60S ribosomal protein L30, uL1, 60S ribosomal protein L3, 60S ribosomal protein L18-A, 60S ribosomal protein L31-A, 60S ribosomal protein L10, 60S ribosomal protein L4-A, 60S ribosomal protein L19-A, 60S ribosomal protein L32, 60S ribosomal protein L20-A, 60S ribosomal protein L5, 60S ribosomal protein L21-A, 60S ribosomal protein L33-A, 60S ribosomal protein L22-A, 60S ribosomal protein L6-A, 60S ribosomal protein L34-A, 60S ribosomal protein L7-A, 60S ribosomal protein L35-A, Eukaryotic translation initiation factor 5A-1/RNA Complex
KeywordsRIBOSOME / cryo-EM / ribosome / RNA / helicase
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
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.
CitationScience, 2016, 354, 1431-1433

Science, 2016, 354, 1431-1433 Yorodumi Papers
The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.
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

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 chain18S ribosomal RNA


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


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


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


Mass: 24815.684 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
#83: RNA chain25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: REF: 831416132
#84: RNA chain5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: GenBank: 1039024045
#85: RNA chain5.8S ribosomal RNA


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

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

#2: Polypeptide(L)40S ribosomal protein S3 / RP13 / YS3


Mass: 26542.789 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05750

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26783

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)40S ribosomal protein S10-A


Mass: 12757.445 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q08745

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)40S ribosomal protein S12


Mass: 15488.631 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P48589

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)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)
References: UniProt: Q01855

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)40S ribosomal protein S16-A / RP61R


Mass: 15877.490 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX51

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)40S ribosomal protein S17-B / RP51B


Mass: 15835.384 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14127

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)40S ribosomal protein S18-A


Mass: 17071.641 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX55

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • rRNA export from nucleus (GO: 0006407)
  • translation (GO: 0006412)
#10: Polypeptide(L)40S ribosomal protein S19-A / RP55A / S16a / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P07280

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)40S ribosomal protein S20


Mass: 13929.044 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38701

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#12: Polypeptide(L)40S ribosomal protein S25-A / RP45 / S31 / YS23


Mass: 12067.272 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q3E792

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)40S ribosomal protein S28-B / S33 / YS27


Mass: 7578.822 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C0X0

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)40S ribosomal protein S29-A / S36 / YS29


Mass: 6675.723 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P41057

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A


Mass: 28051.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P32905

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • ribosomal small subunit assembly (GO: 0000028)
  • rRNA export from nucleus (GO: 0006407)
#18: Polypeptide(L)40S ribosomal protein S1-A / RP10A


Mass: 28798.467 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P33442

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#19: Polypeptide(L)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)
References: UniProt: P25443

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX35

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX37

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • rRNA methylation (GO: 0031167)
#22: Polypeptide(L)40S ribosomal protein S7-A / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26786

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX39

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#24: Polypeptide(L)40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: O13516

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • positive regulation of translational fidelity (GO: 0045903)
  • rRNA methylation (GO: 0031167)
#25: Polypeptide(L)40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX47

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)40S ribosomal protein S13 / S27a / YS15


Mass: 17059.945 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05756

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)40S ribosomal protein S14-A / RP59A


Mass: 14562.655 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P06367

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)40S ribosomal protein S21-A / S26 / YS25


Mass: 9758.829 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C0V8

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
#29: Polypeptide(L)40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C0W1

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX29

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • regulation of translational fidelity (GO: 0006450)
  • translation (GO: 0006412)
#31: Polypeptide(L)40S ribosomal protein S24-A / RP50


Mass: 15362.848 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX31

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#32: Polypeptide(L)40S ribosomal protein S26-A


Mass: 13538.922 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P39938

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)40S ribosomal protein S27-A / RP61 / YS20


Mass: 8893.391 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P35997

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)40S ribosomal protein S30-A


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

Cellular component

Molecular function

Biological process

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Ubiquitin- ... , 2 types, 2 molecules NAO

#15: Polypeptide(L)Ubiquitin-40S ribosomal protein S31


Mass: 17254.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05759

Cellular component

Molecular function

Biological process

#55: Polypeptide(L)Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CH08

Cellular component

Molecular function

Biological process

+
Polypeptide(L) , 4 types, 4 molecules OiAZBT

#16: Polypeptide(L)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)
References: UniProt: P38011

Cellular component

Molecular function

Biological process

  • G-protein coupled receptor signaling pathway (GO: 0007186)
  • invasive growth in response to glucose limitation (GO: 0001403)
  • negative regulation of glucose mediated signaling pathway (GO: 1902660)
  • negative regulation of translation (GO: 0017148)
  • negative regulation of translational frameshifting (GO: 2001125)
#39: Polypeptide(L)Superkiller protein 3


Mass: 163922.141 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P17883

Cellular component

Biological process

  • defense response to virus (GO: 0051607)
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay (GO: 0070478)
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' (GO: 0034427)
  • nuclear-transcribed mRNA catabolic process, non-stop decay (GO: 0070481)
#66: Polypeptide(L)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 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)
#86: Polypeptide(L)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)
References: UniProt: P23301

Cellular component

Molecular function

Biological process

  • positive regulation of cytoplasmic translational elongation through polyproline stretches (GO: 1903272)
  • positive regulation of translational elongation (GO: 0045901)
  • positive regulation of translational initiation (GO: 0045948)
  • positive regulation of translational termination (GO: 0045905)
  • translational frameshifting (GO: 0006452)

+
Antiviral ... , 2 types, 3 molecules hjk

#38: Polypeptide(L)Antiviral helicase SKI2 / Superkiller protein 2


Mass: 146259.094 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P35207, EC: 3.6.4.13

Cellular component

Molecular function

Biological process

  • defense response to virus (GO: 0051607)
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay (GO: 0070478)
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' (GO: 0034427)
  • nuclear-transcribed mRNA catabolic process, non-stop decay (GO: 0070481)
  • posttranscriptional gene silencing (GO: 0016441)
  • potassium ion transport (GO: 0006813)
  • regulation of translation (GO: 0006417)
  • response to potassium ion (GO: 0035864)
#40: Polypeptide(L)Antiviral protein SKI8 / Superkiller protein 8


Mass: 44283.527 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02793

Cellular component

Biological process

  • cellular protein complex assembly (GO: 0043623)
  • defense response to virus (GO: 0051607)
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay (GO: 0070478)
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' (GO: 0034427)
  • nuclear-transcribed mRNA catabolic process, non-stop decay (GO: 0070481)
  • protein-DNA complex assembly (GO: 0065004)
  • reciprocal meiotic recombination (GO: 0007131)

+
60S ribosomal protein ... , 40 types, 40 molecules AAABACADAEAFAGAHAIAJ...

#41: Polypeptide(L)60S ribosomal protein L8-A / 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)
References: UniProt: P17076

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)60S ribosomal protein L23-A / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX41

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein L36-A / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05745

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05738

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04449

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49166

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
  • translation (GO: 0006412)
#47: Polypeptide(L)60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C0W9

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04456

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49167

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)60S ribosomal protein L13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12690

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)60S ribosomal protein L26-A / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05743

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)60S ribosomal protein L39 / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04650

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)60S ribosomal protein L14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P36105

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)60S ribosomal protein L27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H6

Cellular component

Molecular function

Biological process

#56: Polypeptide(L)60S ribosomal protein L42-A / L41 / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX27

Cellular component

Molecular function

Biological process

#57: Polypeptide(L)60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05748

Cellular component

Molecular function

Biological process

#58: Polypeptide(L)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)
References: UniProt: P02406

Cellular component

Molecular function

Biological process

#59: Polypeptide(L)60S ribosomal protein L41-A / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX86

Cellular component

Molecular function

Biological process

#60: Polypeptide(L)60S ribosomal protein L43-A / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX25

Cellular component

Molecular function

Biological process

#61: Polypeptide(L)60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26784

Cellular component

Molecular function

Biological process

#62: Polypeptide(L)60S ribosomal protein L29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05747

Cellular component

Molecular function

Biological process

#63: Polypeptide(L)60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX45

Cellular component

Molecular function

Biological process

#64: Polypeptide(L)60S ribosomal protein L17-A / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05740

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
#65: Polypeptide(L)60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14120

Cellular component

Molecular function

Biological process

#67: Polypeptide(L)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)
References: UniProt: P14126

Cellular component

Molecular function

Biological process

#68: Polypeptide(L)60S ribosomal protein L18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX49

Cellular component

Molecular function

Biological process

#69: Polypeptide(L)60S ribosomal protein L31-A / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

#70: Polypeptide(L)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)
References: UniProt: P41805

Cellular component

Molecular function

Biological process

#71: Polypeptide(L)60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P10664

Cellular component

Molecular function

Biological process

#72: Polypeptide(L)60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX82

Cellular component

Molecular function

Biological process

#73: Polypeptide(L)60S ribosomal protein L32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38061

Cellular component

Molecular function

Biological process

#74: Polypeptide(L)60S ribosomal protein L20-A / L18a


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX23

Cellular component

Molecular function

Biological process

#75: Polypeptide(L)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)
References: UniProt: P26321

Cellular component

Molecular function

Biological process

#76: Polypeptide(L)60S ribosomal protein L21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02753

Cellular component

Molecular function

Biological process

#77: Polypeptide(L)60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05744

Cellular component

Molecular function

Biological process

#78: Polypeptide(L)60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05749

Cellular component

Molecular function

Biological process

#79: Polypeptide(L)60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02326

Cellular component

Molecular function

Biological process

#80: Polypeptide(L)60S ribosomal protein L34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P87262

Cellular component

Molecular function

Biological process

#81: Polypeptide(L)60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05737

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of LSU-rRNA (GO: 0000470)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • ribosomal large subunit biogenesis (GO: 0042273)
#82: Polypeptide(L)60S ribosomal protein L35-A


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

Cellular component

Molecular function

Biological process

-
Experimental details

-
Experiment

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

-
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 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMHEPESC8H18N2O4S1
2100mMPotassium acetateKOAc1
310mMMagnesium chlorideMgCl21
41mMDTTC4H10O2S21
50.5mMPMSFC7H7FO2S1
610ug/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

-
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 FIELD / 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

-
Processing

EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
1Gautomatch0.53PARTICLE SELECTIONFor details, see http://www.mrc-lmb.cam.ac.uk/kzhang/1
2EM-ToolsIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
8CootMODEL FITTING1
10RELION1.4INITIAL EULER ASSIGNMENT1
12FREALIGN9.11CLASSIFICATION1
13FREALIGN9.11RECONSTRUCTION1
14PHENIX1.10MODEL REFINEMENTReal-space refinement1
15REFMAC5.8MODEL REFINEMENTReciprocal space refinement1
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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