6MTB

Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8G [auth A]248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 8
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60S ribosomal protein L3H [auth B]394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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Entity ID: 9
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60S ribosomal protein L4I [auth C]362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
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60S ribosomal protein L5J [auth D]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
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60S ribosomal protein L6K [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L7L [auth F]247Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L7aM [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
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60S ribosomal protein L9N [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L10O [auth I]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 16
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60S ribosomal protein L11P [auth J]178Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 17
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60S ribosomal protein L13Q [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L14R [auth M]138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 19
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60S ribosomal protein L15S [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L13aT [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L17U [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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60S ribosomal protein L18V [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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60S ribosomal protein L19W [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L18aX [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
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60S ribosomal protein L21Y [auth T]159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 26
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60S ribosomal protein L22Z [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L23AA [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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60S ribosomal protein L24BA [auth W]157Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 29
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60S ribosomal protein L23aCA [auth X]118Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
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60S ribosomal protein L26DA [auth Y]134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 31
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60S ribosomal protein L27EA [auth Z]135Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27
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Entity ID: 32
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60S ribosomal protein L27aFA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L29GA [auth b]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
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60S ribosomal protein L30HA [auth c]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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60S ribosomal protein L31IA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L32JA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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60S ribosomal protein L35aKA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L34LA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L35MA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L36NA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L37OA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L38PA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39QA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
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60S ribosomal protein L40RA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L41SA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L36aTA [auth o]103Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L37aUA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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60S ribosomal protein L28VA [auth r]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
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60S ribosomal protein L10aWA [auth u]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
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40S ribosomal protein SAYA [auth AA]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
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40S ribosomal protein S3aZA [auth BB]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 53
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40S ribosomal protein S2AB [auth CC]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
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40S ribosomal protein S3BB [auth DD]228Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
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40S ribosomal protein S4, X isoformCB [auth EE]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
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40S ribosomal protein S5DB [auth FF]204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 57
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40S ribosomal protein S6EB [auth GG]237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
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40S ribosomal protein S7FB [auth HH]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
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40S ribosomal protein S8GB [auth II]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
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40S ribosomal protein S9HB [auth JJ]185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 61
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40S ribosomal protein S10IB [auth KK]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S11JB [auth LL]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S12KB [auth MM]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
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40S ribosomal protein S13LB [auth NN]149Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
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Entity ID: 65
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40S ribosomal protein S14MB [auth OO]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S15NB [auth PP]120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 67
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40S ribosomal protein S16OB [auth QQ]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S17PB [auth RR]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S18QB [auth SS]144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S19RB [auth TT]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S20SB [auth UU]100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S21TB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S15aUB [auth WW]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S23VB [auth XX]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S24WB [auth YY]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S25XB [auth ZZ]75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26YB [auth aa]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S27ZB [auth bb]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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40S ribosomal protein S28AC [auth cc]62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 80
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40S ribosomal protein S29BC [auth dd]55Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30CC [auth ee]55Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27aDC [auth ff]68Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1EC [auth gg]313Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    mRNAA [auth 1]7unidentified
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    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    P-site tRNAB [auth 2]76Oryctolagus cuniculus
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    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    Z-site tRNAC [auth 4]75Oryctolagus cuniculus
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    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    28S rRNAD [auth 5]3597Oryctolagus cuniculus
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    5S rRNAE [auth 7]120Oryctolagus cuniculus
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    Entity ID: 6
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    5.8S rRNAF [auth 8]151Oryctolagus cuniculus
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    Entity ID: 50
    MoleculeChainsLengthOrganismImage
    18S rRNAXA [auth 9]1698Oryctolagus cuniculus
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    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    PK [auth g], QK [auth j], RK [auth m], SK [auth o], TK [auth p], VN [auth aa], WN [auth dd], XN [auth ff]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 5] , AH [auth 5] , AI [auth 5] , AJ [auth 5] , AK [auth 7] , 
    AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth 5],  AJ [auth 5],  AK [auth 7],  AL [auth 9],  AM [auth 9],  AN [auth 9],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 5],  BI [auth 5],  BJ [auth 5],  BK [auth 7],  BL [auth 9],  BM [auth 9],  BN [auth 9],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 5],  CI [auth 5],  CJ [auth 5],  CK [auth 7],  CL [auth 9],  CM [auth 9],  CN [auth 9],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 5],  DI [auth 5],  DJ [auth 5],  DK [auth 8],  DL [auth 9],  DM [auth 9],  DN [auth 9],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 5],  EI [auth 5],  EJ [auth 5],  EK [auth 8],  EL [auth 9],  EM [auth 9],  EN [auth 9],  FC [auth 5],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 5],  FI [auth 5],  FJ [auth 5],  FK [auth 8],  FL [auth 9],  FM [auth 9],  FN [auth 9],  GC [auth 5],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 5],  GI [auth 5],  GJ [auth 5],  GK [auth 8],  GL [auth 9],  GM [auth 9],  GN [auth 9],  HC [auth 5],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 5],  HI [auth 5],  HJ [auth 5],  HK [auth 8],  HL [auth 9],  HM [auth 9],  HN [auth 9],  IC [auth 5],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 5],  II [auth 5],  IJ [auth 5],  IK [auth 8],  IL [auth 9],  IM [auth 9],  IN [auth 9],  JC [auth 5],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  JI [auth 5],  JJ [auth 5],  JK [auth 8],  JL [auth 9],  JM [auth 9],  JN [auth 9],  KC [auth 5],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth 5],  KJ [auth 5],  KK [auth A],  KL [auth 9],  KM [auth 9],  KN [auth 9],  LC [auth 5],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  LI [auth 5],  LJ [auth 5],  LK [auth P],  LL [auth 9],  LM [auth 9],  LN [auth 9],  MC [auth 5],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  MI [auth 5],  MJ [auth 5],  MK [auth Q],  ML [auth 9],  MM [auth 9],  MN [auth 9],  NC [auth 5],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  NI [auth 5],  NJ [auth 5],  NK [auth V],  NL [auth 9],  NM [auth 9],  NN [auth 9],  OC [auth 5],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  OI [auth 5],  OJ [auth 5],  OK [auth a],  OL [auth 9],  OM [auth 9],  ON [auth 9],  PC [auth 5],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth 5],  PI [auth 5],  PJ [auth 5],  PL [auth 9],  PM [auth 9],  PN [auth 9],  QC [auth 5],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth 5],  QI [auth 5],  QJ [auth 5],  QL [auth 9],  QM [auth 9],  QN [auth 9],  RC [auth 5],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth 5],  RI [auth 5],  RJ [auth 5],  RL [auth 9],  RM [auth 9],  RN [auth 9],  SC [auth 5],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth 5],  SI [auth 5],  SJ [auth 5],  SL [auth 9],  SM [auth 9],  SN [auth 9],  TC [auth 5],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth 5],  TI [auth 5],  TJ [auth 5],  TL [auth 9],  TM [auth 9],  TN [auth 9],  UC [auth 5],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth 5],  UI [auth 5],  UJ [auth 5],  UK [auth 9],  UL [auth 9],  UM [auth 9],  UN [auth aa],  VC [auth 5],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth 5],  VI [auth 5],  VJ [auth 5],  VK [auth 9],  VL [auth 9],  VM [auth 9],  WC [auth 5],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth 5],  WI [auth 5],  WJ [auth 7],  WK [auth 9],  WL [auth 9],  WM [auth 9],  XC [auth 5],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth 5],  XI [auth 5],  XJ [auth 7],  XK [auth 9],  XL [auth 9],  XM [auth 9],  YC [auth 5],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth 5],  YI [auth 5],  YJ [auth 7],  YK [auth 9],  YL [auth 9],  YM [auth 9],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth 5],  ZI [auth 5],  ZJ [auth 7],  ZK [auth 9],  ZL [auth 9],  ZM [auth 9]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MLZ
    Query on MLZ
    I [auth C]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • 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