6FXC

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.

Matzov, D.Aibara, S.Basu, A.Zimmerman, E.Bashan, A.Yap, M.F.Amunts, A.Yonath, A.E.

(2017) Nat Commun 8: 723-723

  • DOI: 10.1038/s41467-017-00753-8
  • Primary Citation of Related Structures:  
    5NGM, 6FXC

  • PubMed Abstract: 
  • Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S ...

    Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.


    Organizational Affiliation

    Faculty of Chemistry, Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel. ada.yonath@weizmann.ac.il.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth Ab],
BB [auth Bb]
226Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsBSAB1118
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth Ac],
CB [auth Bc]
202Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsCSAB2116c
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth Ad],
DB [auth Bd]
198Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsDSAB1578
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth Ae],
EB [auth Be]
156Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsESAB2105c
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth Af],
FB [auth Bf]
95Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsFSAB0316
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth Ag],
GB [auth Bg]
152Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077VHU6 (Staphylococcus schweitzeri)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth Ah],
HB [auth Bh]
131Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsHSAB2108c
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth Ai],
IB [auth Bi]
127Staphylococcus aureusMutation(s): 0 
Gene Names: rpsIA6762_11315BTN44_13505EP54_02240EQ90_01125QU38_03565SA0759_03288SA950122_03152
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth Aj],
JB [auth Bj]
97Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsJSAB2123c
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth Ak],
KB [auth Bk]
114Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsKSAB2098c
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth Al],
LB [auth Bl]
135Staphylococcus aureusMutation(s): 0 
Gene Names: rpsLHMPREF3211_01391SAJPND4_00536
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth Am],
MB [auth Bm]
121Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsMSAB2099c
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth An],
NB [auth Bn]
60Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsZrpsN1SAB2109c
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth Ao],
OB [auth Bo]
88Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsOSAB1135
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth Ap],
PB [auth Bp]
89Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsPSAB1102
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth Aq],
QB [auth Bq]
80Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsQSAB2113c
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth Ar],
RB [auth Br]
54Staphylococcus aureusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth As],
SB [auth Bs]
80Staphylococcus aureusMutation(s): 0 
Gene Names: rpsSHMPREF3211_01571SAJPND4_02217
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth At],
TB [auth Bt]
81Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsTSAB1458
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth Au],
UB [auth Bu]
52Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpsUSAB1447c
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promotion factorV [auth Av],
VB [auth Bv]
190Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: hpfSAB0704
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth AC],
YB [auth BC]
274Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplBSAB2119c
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth AD],
ZB [auth BD]
215Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplCSAB2122c
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth AE],
AC [auth BE]
206Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplDSAB2121c
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth AF],
BC [auth BF]
175Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplESAB2110c
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth AG],
CC [auth BG]
175Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplFSAB2107c
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth AH],
DC [auth BH]
145Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplMSAB2091c
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth AI],
EC [auth BI]
122Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplNSAB2112c
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth AJ],
FC [auth BJ]
146Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplOSAB2103c
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth AK],
GC [auth BK]
137Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplPSAB2115c
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth AL],
HC [auth BL]
120Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplQSAB2096c
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18IA [auth AM],
IC [auth BM]
119Staphylococcus aureusMutation(s): 0 
Gene Names: 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth AN],
JC [auth BN]
114Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplSSAB1105
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20KA [auth AO],
KC [auth BO]
116Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplTSAB1538c
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21LA [auth AP],
LC [auth BP]
102Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplUSAB1516c
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22MA [auth AQ],
MC [auth BQ]
112Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplVSAB2117c
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth AR],
NC [auth BR]
89Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplWSAB2120c
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24OA [auth AS],
OC [auth BS]
103Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rplXSAB2111c
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25PA [auth AT],
PC [auth BT]
94Staphylococcus aureusMutation(s): 0 
Gene Names: rplYctcHMPREF3211_00359
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UniProt GroupA0A133Q8Z9
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth AU],
QC [auth BU]
82Staphylococcus aureusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28RA [auth AV],
RC [auth BV]
58Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpmBSAB1088c
UniProt
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29SA [auth AW],
SC [auth BW]
67Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpmCSAB2114c
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth AX],
TC [auth BX]
58Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpmDSAB2104c
UniProt
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BUA [auth AY],
UC [auth BY]
59Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpmE2SAB2004c
UniProt
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth AZ],
VC [auth BZ]
48Staphylococcus aureusMutation(s): 0 
Gene Names: rpmFBSZ10_12860
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33WA [auth A1],
WC [auth B1]
47Staphylococcus aureusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34XA [auth A2],
XC [auth B2]
43Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpmHSAB2590c
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35YA [auth A3],
YC [auth B3]
64Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: rpmISAB1539c
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36ZA [auth A4],
ZC [auth B4]
37Staphylococcus aureusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth Aa],
AB [auth Ba]
1,539Staphylococcus aureus
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Entity ID: 23
MoleculeChainsLengthOrganismImage
23S ribosomal RNAW [auth AA],
WB [auth BA]
2,923Staphylococcus aureus
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Entity ID: 24
MoleculeChainsLengthOrganismImage
5S ribosomal RNAX [auth AB],
XB [auth BB]
115Staphylococcus aureus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenFFL15-0325
European Research CouncilIsrael322581

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations