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


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:  
    6MTB, 6MTC, 6MTD, 6MTE

  • 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.



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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth A]248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 6
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60S ribosomal protein L3F [auth B]394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 7
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60S ribosomal protein L4G [auth C]362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L5H [auth D]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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60S ribosomal protein L6I [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
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60S ribosomal protein L7J [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
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60S ribosomal protein L7aK [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L9L [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L10M [auth I]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 14
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60S ribosomal protein L11N [auth J]170Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 15
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60S ribosomal protein L13O [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L14P [auth M]138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 17
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60S Ribosomal protein L15Q [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L13aR [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L17S [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L18T [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L19U [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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60S ribosomal protein L18aV [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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60S ribosomal protein L21W [auth T]159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 24
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60S ribosomal protein L22X [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
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60S ribosomal protein L23Y [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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60S ribosomal protein L24Z [auth W]157Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 27
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60S ribosomal protein L23aAA [auth X]118Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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60S ribosomal protein L26BA [auth Y]134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 29
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60S ribosomal protein L27CA [auth Z]135Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27
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Entity ID: 30
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60S ribosomal protein L27aDA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
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60S ribosomal protein L29EA [auth b]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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60S ribosomal protein L30FA [auth c]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L31GA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
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60S ribosomal protein L32HA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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60S ribosomal protein L35aIA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L34JA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L35KA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L36LA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L37MA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L38NA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L39OA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L40PA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L41QA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36aRA [auth o]103Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L37aSA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L28TA [auth r]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L10aUA [auth u]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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Interferon-related developmental regulator 2VA [auth v]441Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
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40S ribosomal protein SAXA [auth AA]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
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40S ribosomal protein S3aYA [auth BB]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 52
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40S ribosomal protein S2ZA [auth CC]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
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40S ribosomal protein S3AB [auth DD]228Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
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40S ribosomal protein S4, X isoformBB [auth EE]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
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40S ribosomal protein S5CB [auth FF]204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 56
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40S ribosomal protein S6DB [auth GG]237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
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40S ribosomal protein S7EB [auth HH]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
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40S ribosomal protein S8FB [auth II]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
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40S ribosomal protein S9GB [auth JJ]185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 60
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40S ribosomal protein S10HB [auth KK]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
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40S ribosomal protein S11IB [auth LL]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S12JB [auth MM]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S13KB [auth NN]149Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
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Entity ID: 64
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40S ribosomal protein S14LB [auth OO]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S15MB [auth PP]120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 66
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40S ribosomal protein S16NB [auth QQ]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S17OB [auth RR]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S18PB [auth SS]144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S19QB [auth TT]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S20RB [auth UU]100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S21SB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S15aTB [auth WW]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S23UB [auth XX]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S24VB [auth YY]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S25WB [auth ZZ]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S26XB [auth aa]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S27YB [auth bb]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S28ZB [auth cc]62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 79
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40S ribosomal protein S29AC [auth dd]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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40S ribosomal protein S30BC [auth ee]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
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40S ribosomal protein S27aCC [auth ff]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1DC [auth gg]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Z-site tRNAA [auth 4]75Oryctolagus cuniculus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
28S rRNAB [auth 5]3597Oryctolagus cuniculus
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Entity ID: 3
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5S rRNAC [auth 7]120Oryctolagus cuniculus
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Entity ID: 4
MoleculeChainsLengthOrganismImage
5.8S rRNAD [auth 8]151Oryctolagus cuniculus
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Entity ID: 49
MoleculeChainsLengthOrganismImage
18S rRNAWA [auth 9]1698Oryctolagus cuniculus
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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OK [auth g],
PK [auth j],
QK [auth m],
RK [auth o],
SK [auth p],
OK [auth g],
PK [auth j],
QK [auth m],
RK [auth o],
SK [auth p],
UN [auth aa],
VN [auth dd],
WN [auth ff]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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