5NGM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 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: 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
255Staphylococcus aureusMutation(s): 0 
Gene Names: rpsB (rpsB_1)
Find proteins for A0A077UDU1 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UDU1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
Ac
217Staphylococcus aureusMutation(s): 0 
Gene Names: rpsC (rpsC_1)
Find proteins for A0A077UU26 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UU26
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
Ad
200Staphylococcus aureusMutation(s): 0 
Gene Names: rpsD_2 (rpsD)
Find proteins for W8TVK2 (Staphylococcus aureus)
Go to UniProtKB:  W8TVK2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
Ae
166Staphylococcus aureusMutation(s): 0 
Gene Names: rpsE (rpsE_1)
Find proteins for W8TUC9 (Staphylococcus aureus)
Go to UniProtKB:  W8TUC9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
Af
98Staphylococcus aureusMutation(s): 0 
Gene Names: rpsF (rpsF_1, rpsF_2, rpsF_3, rpsF_4)
Find proteins for W8TPC6 (Staphylococcus aureus)
Go to UniProtKB:  W8TPC6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
Ag
156Staphylococcus 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
132Staphylococcus aureusMutation(s): 0 
Gene Names: rpsH (rpsH_1)
Find proteins for W8U8T8 (Staphylococcus aureus)
Go to UniProtKB:  W8U8T8
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
Ai
132Staphylococcus aureusMutation(s): 0 
Gene Names: rpsI (rpsI_1, rpsI_2, rpsI_4, rpsI_5)
Find proteins for A0A0K7UQP6 (Staphylococcus aureus)
Go to UniProtKB:  A0A0K7UQP6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
Aj
102Staphylococcus aureusMutation(s): 0 
Gene Names: rpsJ (rpsJ_1)
Find proteins for A0A0H2K0A0 (Staphylococcus aureus)
Go to UniProtKB:  A0A0H2K0A0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
Ak
129Staphylococcus aureusMutation(s): 0 
Gene Names: rpsK (rpsK_1, rpsK_2)
Find proteins for A0A077UKD6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKD6
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
Al
137Staphylococcus aureusMutation(s): 0 
Gene Names: rpsL
Find proteins for W8U1C6 (Staphylococcus aureus)
Go to UniProtKB:  W8U1C6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
Am
121Staphylococcus aureusMutation(s): 0 
Gene Names: rpsM (rpsM_1)
Find proteins for W8U8U6 (Staphylococcus aureus)
Go to UniProtKB:  W8U8U6
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
An
61Staphylococcus aureusMutation(s): 0 
Gene Names: rpsN_1 (rpsN, rpsN_2, rpsNA, rpsZ)
Find proteins for A0A077UGW7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGW7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
Ao
89Staphylococcus aureusMutation(s): 0 
Gene Names: rpsO (rpsO_1)
Find proteins for W8U6H8 (Staphylococcus aureus)
Go to UniProtKB:  W8U6H8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
Ap
91Staphylococcus aureusMutation(s): 0 
Gene Names: rpsP_1 (rpsP, rpsP_2)
Find proteins for W8U6K4 (Staphylococcus aureus)
Go to UniProtKB:  W8U6K4
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Aq
87Staphylococcus aureusMutation(s): 0 
Gene Names: rpsQ (rpsQ_1)
Find proteins for A0A077VLD5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VLD5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
Ar
80Staphylococcus aureusMutation(s): 0 
Gene Names: rpsR (rpsR_1, rpsR_2, rpsR_3, rpsR_4)
Find proteins for A0A077UZF4 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UZF4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
As
92Staphylococcus aureusMutation(s): 0 
Gene Names: rpsS (rpsS_1)
Find proteins for A0A077V0P8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V0P8
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
At
83Staphylococcus aureusMutation(s): 0 
Gene Names: rpsT (rpsT_1)
Find proteins for W8UXC3 (Staphylococcus aureus)
Go to UniProtKB:  W8UXC3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
Au
58Staphylococcus aureusMutation(s): 0 
Gene Names: rpsU
Find proteins for A0A077UHS1 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UHS1
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promoting factor
Av
190Staphylococcus aureusMutation(s): 0 
Gene Names: hpf (raiA)
Find proteins for W8USK0 (Staphylococcus aureus)
Go to UniProtKB:  W8USK0
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AC
277Staphylococcus aureusMutation(s): 0 
Gene Names: rplB (rplB_1)
Find proteins for A0A077W1J0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077W1J0
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AD
220Staphylococcus aureusMutation(s): 0 
Gene Names: rplC (rplC_1)
Find proteins for W8U3W0 (Staphylococcus aureus)
Go to UniProtKB:  W8U3W0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AE
207Staphylococcus aureusMutation(s): 0 
Gene Names: rplD (rplD_1)
Find proteins for W8TRC7 (Staphylococcus aureus)
Go to UniProtKB:  W8TRC7
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AF
179Staphylococcus aureusMutation(s): 0 
Gene Names: rplE (rplE_1)
Find proteins for W8TUC3 (Staphylococcus aureus)
Go to UniProtKB:  W8TUC3
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AG
178Staphylococcus aureusMutation(s): 0 
Gene Names: rplF (rplF_1)
Find proteins for W8U3X2 (Staphylococcus aureus)
Go to UniProtKB:  W8U3X2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AH
145Staphylococcus aureusMutation(s): 0 
Gene Names: rplM (rplM_1, rplM_2, rplM_3, rplM_4)
Find proteins for W8TUE6 (Staphylococcus aureus)
Go to UniProtKB:  W8TUE6
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AI
122Staphylococcus aureusMutation(s): 0 
Gene Names: rplN (rplN_1, rplNA)
Find proteins for A0A077UUA0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UUA0
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AJ
146Staphylococcus aureusMutation(s): 0 
Gene Names: rplO (rplO_1)
Find proteins for A0A077UGA7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGA7
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AK
144Staphylococcus aureusMutation(s): 0 
Gene Names: rplP (rplP_1)
Find proteins for A0A077V4G0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V4G0
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AL
122Staphylococcus aureusMutation(s): 0 
Gene Names: rplQ (rplQ_1, rplQ_2)
Find proteins for A0A077UG91 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UG91
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AM
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
116Staphylococcus aureusMutation(s): 0 
Gene Names: rplS (rplS_1, rplS_2)
Find proteins for A0A077UVB6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UVB6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AO
118Staphylococcus aureusMutation(s): 0 
Gene Names: rplT (rplT_2)
Find proteins for A0A077VMP6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VMP6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AP
102Staphylococcus aureusMutation(s): 0 
Gene Names: rplU (rplU_1)
Find proteins for D7URR3 (Staphylococcus aureus)
Go to UniProtKB:  D7URR3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AQ
117Staphylococcus aureusMutation(s): 0 
Gene Names: rplV (rplV_1)
Find proteins for A0A077UKF9 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKF9
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AR
91Staphylococcus aureusMutation(s): 0 
Gene Names: rplW (rplW_1)
Find proteins for W8TUB4 (Staphylococcus aureus)
Go to UniProtKB:  W8TUB4
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AS
105Staphylococcus aureusMutation(s): 0 
Gene Names: rplX (rplX_1)
Find proteins for W8TRD5 (Staphylococcus aureus)
Go to UniProtKB:  W8TRD5
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AT
217Staphylococcus 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
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AV
62Staphylococcus aureusMutation(s): 0 
Gene Names: rpmB (rpmB_1)
Find proteins for A0A077URJ8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077URJ8
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AW
73Staphylococcus aureus (strain Newman)Mutation(s): 0 
Gene Names: rpmC
Find proteins for A0A0H3KED7 (Staphylococcus aureus (strain Newman))
Go to UniProtKB:  A0A0H3KED7
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AX
59Staphylococcus aureusMutation(s): 0 
Gene Names: rpmD (rpmD_1)
Find proteins for W8UVN7 (Staphylococcus aureus)
Go to UniProtKB:  W8UVN7
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
AY
84Staphylococcus aureusMutation(s): 0 
Gene Names: rpmEB (rpmE2, rpmE2_1)
Find proteins for W8TRP5 (Staphylococcus aureus)
Go to UniProtKB:  W8TRP5
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
AZ
57Staphylococcus aureusMutation(s): 0 
Gene Names: rpmF
Find proteins for A0A077UWR7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UWR7
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A1
49Staphylococcus aureusMutation(s): 0 
Gene Names: rpmG2 (rpmG, rpmGA)
Find proteins for A0A077V2P0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V2P0
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A2
45Staphylococcus 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
66Staphylococcus aureusMutation(s): 0 
Gene Names: rpmI (rpmI_2)
Find proteins for A0A077UL47 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UL47
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A4
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 RNAAa1555Staphylococcus aureus
Entity ID: 23
MoleculeChainsLengthOrganism
23S Ribosomal RNAAA2923Staphylococcus aureus
Entity ID: 24
MoleculeChainsLengthOrganism
5S Ribosomal RNAAB115Staphylococcus aureus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AB, AC, AU, AZ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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