5MYJ

Structure of 70S ribosome from Lactococcus lactis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.

Franken, L.E.Oostergetel, G.T.Pijning, T.Puri, P.Arkhipova, V.Boekema, E.J.Poolman, B.Guskov, A.

(2017) Nat Commun 8: 722-722

  • DOI: 10.1038/s41467-017-00718-x
  • Primary Citation of Related Structures:  
    5MYJ

  • PubMed Abstract: 
  • Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we re ...

    Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPF long . The N-terminal domain of HPF long binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPF long binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPF long , and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPF long due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPF long -mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.


    Organizational Affiliation

    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. a.guskov@rug.nl.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2AB255Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsBllmg_2430
Find proteins for A2RNV0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AC217Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsCllmg_2377
Find proteins for A2RNP9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4AD203Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsDllmg_0296
Find proteins for A2RI10 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5AE168Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsEllmg_2364
Find proteins for A2RNN6 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6AF97Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsFllmg_2475
Find proteins for A2RNZ4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 7
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30S ribosomal protein S7AG155Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsGllmg_2557
Find proteins for A2RP73 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8AH132Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsHllmg_2367
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Entity ID: 9
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30S ribosomal protein S9AI130Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsIllmg_2545
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Entity ID: 10
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30S ribosomal protein S10AJ102Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsJllmg_2384
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Entity ID: 11
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30S ribosomal protein S11AK127Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsKllmg_2355
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Entity ID: 12
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30S ribosomal protein S12AL137Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsLllmg_2558
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Entity ID: 13
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30S ribosomal protein S13AM121Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsMllmg_2356
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Entity ID: 14
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30S ribosomal protein S14 type ZAN61Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsZrpsNllmg_2370
Find proteins for A2RNP2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 15
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30S ribosomal protein S15AO89Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsOllmg_2078
Find proteins for A2RMV9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 16
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30S ribosomal protein S16AP90Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsPllmg_0932
Find proteins for A2RJS1 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 17
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30S ribosomal protein S17AQ86Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsQllmg_2374
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Entity ID: 18
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30S ribosomal protein S18AR81Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsRllmg_2473
Find proteins for A2RNZ2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 19
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30S ribosomal protein S19AS92Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsSllmg_2379
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Entity ID: 20
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30S ribosomal protein S20AT77Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsTllmg_1921
Find proteins for A2RMG0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 21
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30S ribosomal protein S21AU58Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsUllmg_0251
Find proteins for A2RHW9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 22
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50S ribosomal protein L28B064Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmBllmg_0204
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Entity ID: 23
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50S ribosomal protein L29B169Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmCllmg_2375
Find proteins for A2RNP7 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 24
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50S ribosomal protein L30B259Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmDllmg_2363
Find proteins for A2RNN5 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 25
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50S ribosomal protein L31 type BB381Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmE2llmg_0906
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32B457Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmFllmg_0099
Find proteins for A2RHH0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 3B549Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmG3rpmGCllmg_2390
Find proteins for A2RNR2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 28
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50S ribosomal protein L34B644Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmHllmg_0145
Find proteins for A2RHL6 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35B766Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmIllmg_2030
Find proteins for A2RMR2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 30
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50S ribosomal protein L36B838Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmJllmg_2357
Find proteins for A2RNN0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 33
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50S ribosomal protein L2BD276Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplBllmg_2380
Find proteins for A2RNQ2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 34
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50S ribosomal protein L3BE207Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplCllmg_2383
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Entity ID: 35
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50S ribosomal protein L4BF208Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplDllmg_2382
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Entity ID: 36
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50S ribosomal protein L5BG180Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplEllmg_2371
Find proteins for A2RNP3 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 37
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50S ribosomal protein L6BH178Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplFllmg_2366
Find proteins for A2RNN8 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 38
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50S ribosomal protein L13BM148Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplMllmg_2546
Find proteins for A2RP62 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 39
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50S ribosomal protein L14BN122Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplNllmg_2373
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Entity ID: 40
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50S ribosomal protein L15BO147Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplOllmg_2362
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Entity ID: 41
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50S ribosomal protein L16BP137Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplPllmg_2376
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Entity ID: 42
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50S ribosomal protein L17BQ126Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplQllmg_2353
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Entity ID: 43
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50S ribosomal protein L18BR115Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplRllmg_2365
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Entity ID: 44
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50S ribosomal protein L19BS114Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplSllmg_1671
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Entity ID: 45
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50S ribosomal protein L20BT119Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplTllmg_2029
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Entity ID: 46
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50S ribosomal protein L21BU104Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplUllmg_1493
Find proteins for A2RLA4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 47
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50S ribosomal protein L22BV115Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplVllmg_2378
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Entity ID: 48
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50S ribosomal protein L23BW97Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplWllmg_2381
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Entity ID: 49
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50S ribosomal protein L24BX101Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplXllmg_2372
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Entity ID: 50
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50S ribosomal protein L27BZ94Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmAllmg_1491
Find proteins for A2RLA2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 51
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Ribosome hibernation promotion factorA185Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: hpfyfiAllmg_0616
Find proteins for A2RIX0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 1
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16S ribosomal RNAAA1535Lactococcus lactis subsp. cremoris MG1363
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Entity ID: 31
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23S ribosomal RNABA2897Lactococcus lactis subsp. cremoris MG1363
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Entity ID: 32
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5S ribosomal RNABB115Lactococcus lactis subsp. cremoris MG1363
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlandsTOPGO L.10.060
European Research CouncilNetherlandsERC-2014-ADG

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release