6FXC image
Entry Detail
PDB ID:
6FXC
Keywords:
Title:
The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus
Biological Source:
PDB Version:
Deposition Date:
2018-03-08
Release Date:
2018-03-21
Method Details:
Experimental Method:
Resolution:
6.76 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:WA (auth: A1), WC (auth: B1)
Chain Length:47
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:XA (auth: A2), XC (auth: B2)
Chain Length:43
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:YA (auth: A3), YC (auth: B3)
Chain Length:64
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:ZA (auth: A4), ZC (auth: B4)
Chain Length:37
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:W (auth: AA), WB (auth: BA)
Chain Length:1539
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:X (auth: AB), XB (auth: BB)
Chain Length:226
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:Y (auth: AC), YB (auth: BC)
Chain Length:202
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:Z (auth: AD), ZB (auth: BD)
Chain Length:215
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:AA (auth: AE), AC (auth: BE)
Chain Length:206
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:BA (auth: AF), BC (auth: BF)
Chain Length:175
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:CA (auth: AG), CC (auth: BG)
Chain Length:175
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:DA (auth: AH), DC (auth: BH)
Chain Length:145
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:EA (auth: AI), EC (auth: BI)
Chain Length:127
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:FA (auth: AJ), FC (auth: BJ)
Chain Length:97
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:GA (auth: AK), GC (auth: BK)
Chain Length:114
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:HA (auth: AL), HC (auth: BL)
Chain Length:120
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:IA (auth: AM), IC (auth: BM)
Chain Length:119
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:JA (auth: AN), JC (auth: BN)
Chain Length:60
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:KA (auth: AO), KC (auth: BO)
Chain Length:88
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:LA (auth: AP), LC (auth: BP)
Chain Length:89
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:MA (auth: AQ), MC (auth: BQ)
Chain Length:112
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:NA (auth: AR), NC (auth: BR)
Chain Length:54
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:OA (auth: AS), OC (auth: BS)
Chain Length:80
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:PA (auth: AT), PC (auth: BT)
Chain Length:94
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:QA (auth: AU), QC (auth: BU)
Chain Length:52
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:RA (auth: AV), RC (auth: BV)
Chain Length:58
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:SA (auth: AW), SC (auth: BW)
Chain Length:67
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:TA (auth: AX), TC (auth: BX)
Chain Length:58
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31 type B
Chain IDs:UA (auth: AY), UC (auth: BY)
Chain Length:59
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:VA (auth: AZ), VC (auth: BZ)
Chain Length:48
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:A (auth: Aa), AB (auth: Ba)
Chain Length:1539
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:B (auth: Ab), BB (auth: Bb)
Chain Length:226
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:C (auth: Ac), CB (auth: Bc)
Chain Length:202
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:D (auth: Ad), DB (auth: Bd)
Chain Length:215
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:E (auth: Ae), EB (auth: Be)
Chain Length:206
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:F (auth: Af), FB (auth: Bf)
Chain Length:175
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:G (auth: Ag), GB (auth: Bg)
Chain Length:175
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:H (auth: Ah), HB (auth: Bh)
Chain Length:145
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:I (auth: Ai), IB (auth: Bi)
Chain Length:127
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:J (auth: Aj), JB (auth: Bj)
Chain Length:97
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:K (auth: Ak), KB (auth: Bk)
Chain Length:114
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:L (auth: Al), LB (auth: Bl)
Chain Length:120
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:M (auth: Am), MB (auth: Bm)
Chain Length:119
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14 type Z
Chain IDs:N (auth: An), NB (auth: Bn)
Chain Length:60
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:O (auth: Ao), OB (auth: Bo)
Chain Length:88
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:P (auth: Ap), PB (auth: Bp)
Chain Length:89
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:Q (auth: Aq), QB (auth: Bq)
Chain Length:112
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:R (auth: Ar), RB (auth: Br)
Chain Length:54
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:S (auth: As), SB (auth: Bs)
Chain Length:80
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:T (auth: At), TB (auth: Bt)
Chain Length:94
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:U (auth: Au), UB (auth: Bu)
Chain Length:52
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Polymer Type:polypeptide(L)
Description:Ribosome hibernation promotion factor
Chain IDs:V (auth: Av), VB (auth: Bv)
Chain Length:58
Number of Molecules:2
Biological Source:Staphylococcus aureus (strain bovine RF122 / ET3-1)
Ligand Molecules
Primary Citation
The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Nat Commun 8 723 723 (2017)
PMID: 28959035 DOI: 10.1038/s41467-017-00753-8

Abstact

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.

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