5MC6 | pdb_00005mc6

Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.

Schmidt, 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.

(2016) Science 354: 1431-1433

  • DOI: https://doi.org/10.1126/science.aaf7520
  • Primary Citation of Related Structures:  
    5MC6

  • PubMed 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 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.

    • Organizational Affiliation: 

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3B [auth A]240Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5C [auth B]225Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AD [auth C]105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12E [auth D]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15F [auth E]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AG [auth F]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-BH [auth G]136Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AI [auth H]146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AJ [auth I]144Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20K [auth J]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AL [auth K]108Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-BM [auth L]67Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AN [auth M]56Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31O [auth N]152Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinP [auth O]319Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AQ [auth P]252Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AR [auth Q]255Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2S [auth R]254Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AT [auth S]261Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AU [auth T]236Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AV [auth U]190Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AW [auth V]200Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AX [auth W]197Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AY [auth X]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13Z [auth Y]151Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AAA [auth Z]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-ABA [auth a]87Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-ACA [auth b]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ADA [auth c]145Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AEA [auth d]135Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-AFA [auth e]119Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AGA [auth f]82Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AHA [auth g]63Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral helicase SKI2LA [auth h]1,287Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Superkiller protein 3MA [auth i]1,432Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral protein SKI8NA [auth j],
OA [auth k]		397Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-APA [auth AA]256Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AQA [auth AB]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ARA [auth AC]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ASA [auth AD]191Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-ATA [auth AE]155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AUA [auth AF]88Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AVA [auth AG]174Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25WA [auth AH]142Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38XA [auth AI]78Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AYA [auth AJ]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AZA [auth AK]127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39AB [auth AL]51Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-ABB [auth AM]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ACB [auth AN]136Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40DB [auth AO]128Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AEB [auth AP]106Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AFB [auth AQ]204Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28GB [auth AR]149Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AHB [auth AS]25Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AIB [auth AT]92Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AJB [auth AU]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KB [auth AV]59Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-ALB [auth AW]254Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AMB [auth AX]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30NB [auth AY]105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uL1OB [auth AZ]210Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3PB [auth BA]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AQB [auth BB]186Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ARB [auth BC]113Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10SB [auth BD]221Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-ATB [auth BE]362Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AUB [auth BF]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32VB [auth BG]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AWB [auth BH]172Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5XB [auth BI]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AYB [auth BJ]160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AZB [auth BK]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AAC [auth BL]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-ABC [auth BM]176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ACC [auth BN]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ADC [auth BO]244Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AEC [auth BP]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A-1IC [auth BT]157Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth 2]1,800Saccharomyces cerevisiae S288C
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Entity ID: 35
MoleculeChains LengthOrganismImage
mRNAIA [auth l]34Saccharomyces cerevisiae S288C
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Entity ID: 36
MoleculeChains LengthOrganismImage
A-site tRNAJA [auth m]76Saccharomyces cerevisiae S288C
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Entity ID: 37
MoleculeChains LengthOrganismImage
P-site tRNAKA [auth n]77Saccharomyces cerevisiae S288C
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Entity ID: 83
MoleculeChains LengthOrganismImage
25S ribosomal RNAFC [auth BQ]3,396Saccharomyces cerevisiae S288C
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Entity ID: 84
MoleculeChains LengthOrganismImage
5S ribosomal RNAGC [auth BR]121Saccharomyces cerevisiae S288C
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Entity ID: 85
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAHC [auth BS]158Saccharomyces cerevisiae S288C
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
5CT
Query on 5CT		IC [auth BT]PEPTIDE LINKINGC10 H23 N3 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTPHENIX1.10
MODEL REFINEMENTREFMAC5.8

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Other