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:  

  • 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. Gr ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
Ab, Bb
226Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsB
Find proteins for Q2YXL2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXL2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
Ac, Bc
202Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsC
Find proteins for Q2YYQ2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYQ2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
Ad, Bd
198Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsD
Find proteins for Q2YTH0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YTH0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
Ae, Be
156Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q2YYL4 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL4
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
Af, Bf
95Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q2YVJ2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YVJ2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
Ag, Bg
152Staphylococcus aureusMutation(s): 0 
Gene Names: rpsG (rpsG_1)
Find proteins for A0A077VHU6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VHU6
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
Ah, Bh
131Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsH
Find proteins for Q2YYL1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
Ai, Bi
127Staphylococcus aureusMutation(s): 0 
Gene Names: rpsI
Find proteins for A0A1Q4GY48 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q4GY48
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
Aj, Bj
97Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q2YYP5 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
Ak, Bk
114Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsK
Find proteins for Q2YYM1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
Al, Bl
135Staphylococcus aureusMutation(s): 0 
Gene Names: rpsL
Find proteins for A0A133PZQ5 (Staphylococcus aureus)
Go to UniProtKB:  A0A133PZQ5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
Am, Bm
121Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsM
Find proteins for Q2YYM0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM0
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
An, Bn
60Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsZ (rpsN1)
Find proteins for Q2YYL0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
Ao, Bo
88Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q2YXP3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXP3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
Ap, Bp
89Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q2YXH8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXH8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Aq, Bq
80Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for Q2YYK6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
Ar, Br
54N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
As, Bs
80Staphylococcus aureusMutation(s): 0 
Gene Names: rpsS
Find proteins for A0A133PYC3 (Staphylococcus aureus)
Go to UniProtKB:  A0A133PYC3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
At, Bt
81Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsT
Find proteins for Q2YT41 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YT41
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
Au, Bu
52Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q2YT04 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YT04
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
Av, Bv
190Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: hpf
Find proteins for Q2YSH7 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YSH7
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AC, BC
274Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplB
Find proteins for Q2YYP9 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP9
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AD, BD
215Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2YYP6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AE, BE
206Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2YYP7 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP7
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AF, BF
175Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q2YYK9 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AG, BG
175Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q2YYL2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AH, BH
145Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2YYM8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AI, BI
122Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2YYK7 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AJ, BJ
146Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q2YYL6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AK, BK
137Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2YYQ3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYQ3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AL, BL
120Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2YYM3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM3
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AM, BM
119Staphylococcus aureusMutation(s): 0 
Gene Names: rplR (rplR_1)
Find proteins for W8TRE0 (Staphylococcus aureus)
Go to UniProtKB:  W8TRE0
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AN, BN
114Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2YXM4 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXM4
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AO, BO
116Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2YTB1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YTB1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AP, BP
102Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2YT83 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YT83
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AQ, BQ
112Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2YYQ1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYQ1
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AR, BR
89Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2YYP8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP8
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AS, BS
103Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2YYK8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AT, BT
94Staphylococcus aureusMutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0A133Q8Z9 (Staphylococcus aureus)
Go to UniProtKB:  A0A133Q8Z9
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AU, BU
82N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AV, BV
58Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q2YXJ2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXJ2
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AW, BW
67Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2YYN0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYN0
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AX, BX
58Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q2YYL5 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL5
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
AY, BY
59Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmE2
Find proteins for Q2YUN3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YUN3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
AZ, BZ
48Staphylococcus aureusMutation(s): 0 
Gene Names: rpmF
Find proteins for A0A1Q8DAT0 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q8DAT0
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A1, B1
47Staphylococcus aureusMutation(s): 0 
Gene Names: rpmG2 (rpmG, rpmG_1, rpmGA)
Find proteins for A0A077V2P0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V2P0
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A2, B2
43Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2YZB6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YZB6
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A3, B3
64Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2YTB0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YTB0
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A4, B4
37Staphylococcus aureusMutation(s): 0 
Gene Names: rpmJ (rpmJ_1)
Find proteins for A0A077UGV8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGV8
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAa,Ba1539Staphylococcus aureus
Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNAAA,BA2923Staphylococcus aureus
Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNAAB,BB115Staphylococcus aureus
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 or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenFFL15-0325
European Research CouncilIsrael322581

Revision History 

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