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


This is version 1.1 of the entry. See complete history


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: https://doi.org/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 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 Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB]255Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC]217Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD]203Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE]168Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF]97Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG]155Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH]132Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI]130Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ]102Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK]127Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL]137Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM]121Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth AN]61Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO]89Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP]90Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ]86Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR]81Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS]92Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT]77Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU]58Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth B0]64Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth B1]69Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth B2]59Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BY [auth B3]81Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth B4]57Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 3AA [auth B5]49Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth B6]44Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth B7]66Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth B8]38Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2GA [auth BD]276Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3HA [auth BE]207Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4IA [auth BF]208Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5JA [auth BG]180Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6KA [auth BH]178Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13LA [auth BM]148Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14MA [auth BN]122Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15NA [auth BO]147Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16OA [auth BP]137Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17PA [auth BQ]126Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18QA [auth BR]115Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19RA [auth BS]114Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RLS5 (Lactococcus lactis subsp. cremoris (strain MG1363))
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UniProt GroupA2RLS5
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20SA [auth BT]119Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RMR1 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21TA [auth BU]104Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RLA4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22UA [auth BV]115Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RNQ0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23VA [auth BW]97Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RNQ3 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24WA [auth BX]101Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RNP4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27XA [auth BZ]94Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RLA2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome hibernation promotion factorYA [auth A]185Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
UniProt
Find proteins for A2RIX0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA]1,535Lactococcus cremoris subsp. cremoris MG1363
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Entity ID: 31
MoleculeChains LengthOrganismImage
23S ribosomal RNAEA [auth BA]2,897Lactococcus cremoris subsp. cremoris MG1363
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Entity ID: 32
MoleculeChains LengthOrganismImage
5S ribosomal RNAFA [auth BB]115Lactococcus cremoris subsp. cremoris MG1363
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references