6MTC

Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structures of translationally inactive mammalian ribosomes.

Brown, A.Baird, M.R.Yip, M.C.Murray, J.Shao, S.

(2018) Elife 7

  • DOI: 10.7554/eLife.40486
  • Primary Citation of Related Structures:  
    6MTE, 6MTB, 6MTD, 6MTC

  • PubMed Abstract: 
  • The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation ...

    The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.


    Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, United States.



Macromolecules

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5D293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13L210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S Ribosomal protein L15N203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19R180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18aS176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22U99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23V131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26Y134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32e128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L36i102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37ap91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-related developmental regulator 2v441Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAAA217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
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40S ribosomal protein S4, X isoformEE262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
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40S ribosomal protein S6GG237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
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40S ribosomal protein S9JJ185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11LL158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S13NN149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S20UU100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S23XX141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S24YY124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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40S ribosomal protein S29dd55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30ee55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7F225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7aG319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9H190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L10I214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 14
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60S ribosomal protein L11J170Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14M138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 18
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60S ribosomal protein L13aO199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17P153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18Q187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21T159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24W157Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23aX118Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27Z135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27aa147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29b245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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60S ribosomal protein L30c98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L31d107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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60S ribosomal protein L35af109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L34g114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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60S ribosomal protein L35h122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L37j86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38k69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L39l50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L40m52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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60S ribosomal protein L41n25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
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60S ribosomal protein L36ao103Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L28r124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L10au206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
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60S ribosomal protein L8A248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 51
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40S ribosomal protein S3aBB213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 52
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40S ribosomal protein S2CC221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
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40S ribosomal protein S3DD228Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
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40S ribosomal protein S5FF204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 57
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40S ribosomal protein S7HH194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
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40S ribosomal protein S8II206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L3B394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
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40S ribosomal protein S10KK96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S12MM117Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 64
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40S ribosomal protein S14OO136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S15PP120Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16QQ142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S17RR132Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 68
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40S ribosomal protein S18SS144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S19TT141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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60S ribosomal protein L4C362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 71
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40S ribosomal protein S21VV83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S15aWW129Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 75
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40S ribosomal protein S25ZZ75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 76
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40S ribosomal protein S26aa101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S27bb83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S28cc62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 81
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40S ribosomal protein S27aff68Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 82
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Receptor of activated protein C kinase 1gg313Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 9
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60S ribosomal protein L6E291Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 1
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Z-site tRNA475Oryctolagus cuniculus
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Entity ID: 2
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28S rRNA53597Oryctolagus cuniculus
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Entity ID: 3
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5S rRNA7120Oryctolagus cuniculus
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Entity ID: 4
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5.8S rRNA8151Oryctolagus cuniculus
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Entity ID: 49
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18S rRNA91698Oryctolagus cuniculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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aa, dd, ff, g, j, m, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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5, 7, 8, 9, A, LL, P, V, aa
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
mL-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2019-05-15
    Changes: Atomic model, Data collection, Derived calculations, Polymer sequence