6TNU

Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Ccr4-Not complex monitors the translating ribosome for codon optimality.

Buschauer, R.Matsuo, Y.Sugiyama, T.Chen, Y.H.Alhusaini, N.Sweet, T.Ikeuchi, K.Cheng, J.Matsuki, Y.Nobuta, R.Gilmozzi, A.Berninghausen, O.Tesina, P.Becker, T.Coller, J.Inada, T.Beckmann, R.

(2020) Science 368

  • DOI: 10.1126/science.aay6912
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping ...

    Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de toshifumi.inada.a3@tohoku.ac.jp jmc71@case.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-AP206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-AQ232Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2R216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3A222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-AS258Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Rps5pB206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5GI526_G0003357
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-AT228Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-AU184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8V187Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-AW184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-AC92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-AX142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12D121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13Y150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-BZ127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-AF141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-BG125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-AH145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-AI143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-Aa87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-Ab129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-Ac144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-Ad134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-AK82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-Be97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-Af81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-AM53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31N73Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like proteinO312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-AL63Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AAW251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3BA386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-ABE361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5BI294Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-BBM175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-ABO222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AAA233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AAD191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10BD218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-BAG169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AAJ193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AAM136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AAQ203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-ABB185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-ABF188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-ABH171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-ABJ159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-ABL100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-AAE126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25AH121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-AAK125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-AAN135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28AR148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29AV58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30AY96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-ABC109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32BG127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-ABN112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-ABP119Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-AAC99Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-AAF81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38AI77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39AL50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-AAS25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-AAP103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-AAT91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 5A-1eI154Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1BT210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20J100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-Ag60Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15E117Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AAU197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AAX183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-AAB136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-ABK106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40AO52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNA21798Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganism
mRNAl6Saccharomyces cerevisiae

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Entity ID: 24
MoleculeChainsLengthOrganism
P-site tRNAn75Saccharomyces cerevisiae

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Entity ID: 37
MoleculeChainsLengthOrganism
A-site tRNAm76Saccharomyces cerevisiae

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Entity ID: 38
MoleculeChainsLengthOrganism
25S rRNABQ3184Saccharomyces cerevisiae

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Entity ID: 39
MoleculeChainsLengthOrganism
5S rRNABR121Saccharomyces cerevisiae

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Entity ID: 40
MoleculeChainsLengthOrganism
5.8S rRNABS158Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE

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BQ
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
 Ligand Interaction
SPD
Query on SPD

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BQ
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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AF, AO, AP, AT, BN, M, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CT
Query on 5CT
eIPEPTIDE LINKINGC10 H23 N3 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBE1814/15-1

Revision History 

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references