5ND8

Hibernating ribosome from Staphylococcus aureus (Unrotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.

Khusainov, I.Vicens, Q.Ayupov, R.Usachev, K.Myasnikov, A.Simonetti, A.Validov, S.Kieffer, B.Yusupova, G.Yusupov, M.Hashem, Y.

(2017) EMBO J 36: 2073-2087

  • DOI: 10.15252/embj.201696105
  • Primary Citation of Related Structures:  
    5ND8, 5ND9, 5NKO

  • PubMed Abstract: 
  • In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy ...

    In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials.


    Organizational Affiliation

    CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France marat@igbmc.fr y.hashem@ibmc-cnrs.unistra.fr.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]255Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsBSAOUHSC_01232
UniProt
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsCSAOUHSC_02506
UniProt
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsDSAOUHSC_01829
UniProt
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsESAOUHSC_02494
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]98Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsFSAOUHSC_00348
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsGSAOUHSC_00528
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsHSAOUHSC_02498
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsISAOUHSC_02477
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]129Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsKSAOUHSC_02486
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]137Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsLSAOUHSC_00527
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]121Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsMSAOUHSC_02487
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth n]61Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsZrpsN1SAOUHSC_02499
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsOSAOUHSC_01250
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsPSAOUHSC_01208
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]87Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsQSAOUHSC_02503
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsRSAOUHSC_00350
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]92Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsSSAOUHSC_02508
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsTSAOUHSC_01689
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth u]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsUSAOUHSC_01678
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promotion factorV [auth v]190Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: hpfSAOUHSC_00767
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth D]277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth E]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth F]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth G]179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth H]178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth M]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth N]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth O]146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth P]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth Q]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
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Entity ID: 35
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50S ribosomal protein L18IA [auth R]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth S]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20KA [auth T]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21LA [auth U]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22MA [auth V]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth W]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
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Entity ID: 41
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50S ribosomal protein L24OA [auth X]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
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Entity ID: 42
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50S ribosomal protein L25PA [auth Y]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplYctcSAOUHSC_00474
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Entity ID: 43
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50S ribosomal protein L27QA [auth Z]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
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Entity ID: 44
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50S ribosomal protein L28RA [auth 0]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmBSAOUHSC_01191
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Entity ID: 45
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50S ribosomal protein L29SA [auth 1]69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
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Entity ID: 46
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50S ribosomal protein L30TA [auth 2]59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
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Entity ID: 47
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50S ribosomal protein L31 type BUA [auth 3]84Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmE2SAOUHSC_02361
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Entity ID: 48
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50S ribosomal protein L32VA [auth 4]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmFSAOUHSC_01078
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Entity ID: 49
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50S ribosomal protein L33 2WA [auth 5]49Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmG2SAOUHSC_01651
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Entity ID: 50
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50S ribosomal protein L34XA [auth 6]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
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Entity ID: 51
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50S ribosomal protein L35YA [auth 7]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
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Entity ID: 52
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50S ribosomal protein L36ZA [auth 8]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmJSAOUHSC_02488
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth a]1547Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 23
MoleculeChainsLengthOrganismImage
23S ribosomal RNAW [auth A]2918Staphylococcus aureus subsp. aureus NCTC 8325
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsLengthOrganismImage
5S ribosomal RNAX [auth B]114Staphylococcus aureus subsp. aureus NCTC 8325
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheFranceANR-10-LABX-0036_NETRNA
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheFranceANR-15-CE11-0021-01
Russian Science FoundationRussian Federation16-14-10014
European Research Council294312
French National Research AgencyFranceFDT20140930867

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references, Other
  • Version 1.2: 2017-07-26
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-02-20
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.5: 2019-11-06
    Changes: Data collection
  • Version 1.6: 2019-12-11
    Changes: Other