5NGM

2.9S structure of the 70S ribosome composing the S. aureus 100S complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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. 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth Ab]255Staphylococcus aureusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth Ac]217Staphylococcus aureusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth Ad]200Staphylococcus aureusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth Ae]166Staphylococcus aureusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth Af]98Staphylococcus aureusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth Ag]156Staphylococcus aureusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth Ah]132Staphylococcus aureusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth Ai]132Staphylococcus aureusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth Aj]102Staphylococcus aureusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth Ak]129Staphylococcus aureusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth Al]137Staphylococcus aureusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth Am]121Staphylococcus aureusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth An]61Staphylococcus aureusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth Ao]89Staphylococcus aureusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth Ap]91Staphylococcus aureusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth Aq]87Staphylococcus aureusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth Ar]80Staphylococcus aureusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth As]92Staphylococcus aureusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth At]83Staphylococcus aureusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth Au]58Staphylococcus aureusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome hibernation promoting factorV [auth Av]190Staphylococcus aureusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth AC]277Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth AD]220Staphylococcus aureusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth AE]207Staphylococcus aureusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth AF]179Staphylococcus aureusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth AG]178Staphylococcus aureusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth AH]145Staphylococcus aureusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth AI]122Staphylococcus aureusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth AJ]146Staphylococcus aureusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth AK]144Staphylococcus aureusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth AL]122Staphylococcus aureusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18IA [auth AM]119Staphylococcus aureusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth AN]116Staphylococcus aureusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20KA [auth AO]118Staphylococcus aureusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21LA [auth AP]102Staphylococcus aureusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22MA [auth AQ]117Staphylococcus aureusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth AR]91Staphylococcus aureusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24OA [auth AS]105Staphylococcus aureusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25PA [auth AT]217Staphylococcus aureusMutation(s): 0 
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Find proteins for A0A133Q8Z9 (Staphylococcus aureus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth AU]94Staphylococcus aureusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28RA [auth AV]62Staphylococcus aureusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29SA [auth AW]73Staphylococcus aureusMutation(s): 0 
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Find proteins for A0A0H3KED7 (Staphylococcus aureus (strain Newman))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth AX]59Staphylococcus aureusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BUA [auth AY]84Staphylococcus aureusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth AZ]57Staphylococcus aureusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33WA [auth A1]49Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077V2P0 (Staphylococcus schweitzeri)
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UniProt GroupA0A077V2P0
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34XA [auth A2]45Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q2YZB6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
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UniProt GroupQ2YZB6
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35YA [auth A3]66Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UL47 (Staphylococcus schweitzeri)
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UniProt GroupA0A077UL47
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36ZA [auth A4]37Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UGV8 (Staphylococcus schweitzeri)
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth Aa]1,555Staphylococcus aureus
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S Ribosomal RNAW [auth AA]2,923Staphylococcus aureus
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S Ribosomal RNAX [auth AB]115Staphylococcus aureus
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth AA]
AC [auth AA]
AD [auth AA]
AE [auth AA]
AF [auth AA]
AB [auth AA],
AC [auth AA],
AD [auth AA],
AE [auth AA],
AF [auth AA],
AG [auth AA],
AH [auth AA],
AI [auth AA],
BB [auth AA],
BC [auth AA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth AA],
BH [auth AA],
BI [auth AA],
CB [auth AA],
CC [auth AA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth AA],
CH [auth AA],
CI [auth AA],
DB [auth AA],
DC [auth AA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth AA],
DH [auth AA],
DI [auth AA],
EB [auth AA],
EC [auth AA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth AA],
EH [auth AA],
EI [auth AA],
FB [auth AA],
FC [auth AA],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth AA],
FH [auth AA],
FI [auth AA],
GB [auth AA],
GC [auth AA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth AA],
GH [auth AA],
GI [auth AA],
HB [auth AA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth AA],
HH [auth AA],
HI [auth AA],
IB [auth AA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth AA],
IH [auth AA],
II [auth AA],
JB [auth AA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth AA],
JH [auth AA],
JI [auth AA],
KB [auth AA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth AA],
KH [auth AA],
KI [auth AA],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth AA],
LH [auth AA],
LI [auth AA],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth AA],
MH [auth AA],
MI [auth AA],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth AA],
NH [auth AA],
NI [auth AA],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth AA],
OH [auth AA],
OI [auth AA],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth AA],
PH [auth AA],
PI [auth AA],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth AA],
QH [auth AA],
QI [auth AA],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth AA],
RH [auth AA],
RI [auth AB],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
SF [auth AA],
SG [auth AA],
SH [auth AA],
SI [auth AB],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TE [auth AA],
TF [auth AA],
TG [auth AA],
TH [auth AA],
TI [auth AC],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UE [auth AA],
UF [auth AA],
UG [auth AA],
UH [auth AA],
UI [auth AC],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth AA],
VF [auth AA],
VG [auth AA],
VH [auth AA],
VI [auth AU],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth AA],
WG [auth AA],
WH [auth AA],
WI [auth AZ],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XE [auth AA],
XF [auth AA],
XG [auth AA],
XH [auth AA],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YF [auth AA],
YG [auth AA],
YH [auth AA],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA],
ZE [auth AA],
ZF [auth AA],
ZG [auth AA],
ZH [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-11-28
    Changes: Data collection, Database references