5ND8

Hibernating ribosome from Staphylococcus aureus (Unrotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.

Khusainov, I.Vicens, Q.Ayupov, R.Usachev, K.Myasnikov, A.Simonetti, A.Validov, S.Kieffer, B.Yusupova, G.Yusupov, M.Hashem, Y.

(2017) EMBO J. 36: 2073-2087

  • DOI: 10.15252/embj.201696105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structu ...

    In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
255Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsB
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ25
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
217Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsC
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW12
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
200Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsD
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXK6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
166Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW23
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
98Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q2G113 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G113
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P48940 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P48940
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsH
Find proteins for Q2FW20 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW20
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
132Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsI
Find proteins for Q2FW39 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW39
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
102Staphylococcus aureus (strain Mu3 / ATCC 700698)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for A7X5G6 (Staphylococcus aureus (strain Mu3 / ATCC 700698))
Go to UniProtKB:  A7X5G6
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
129Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsK
Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW31
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
137Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsL
Find proteins for P0A0H0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0H0
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
121Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsM
Find proteins for Q2FW30 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW30
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
61Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsZ (rpsN1)
Find proteins for Q2FW19 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW19
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G2Q1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
91Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ45
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
87Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW15
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
80Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q2G111 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G111
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
92Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW10
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
83Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsT
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXY6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
58Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q2FXZ7 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXZ7
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
v
190Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: hpf
Find proteins for Q2G055 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G055
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
D
277Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
E
220Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
F
207Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
G
179Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW18
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
H
178Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW21
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
M
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
N
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
O
146Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplO
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
P
144Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
Q
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
R
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
S
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
T
118Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
U
102Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
V
117Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
W
91Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
X
105Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Y
217Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0S0
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
Z
94Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
0
62Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ60
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
1
69Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
2
59Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
3
84Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmE2
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FWD8
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
4
58Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmF
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZF1
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 2
5
49Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmG2
Find proteins for Q2FY22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FY22
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
6
45Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
7
66Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
8
37Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW29
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1547Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNAA2918Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNAB114Staphylococcus aureus subsp. aureus NCTC 8325
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheFranceANR-10-LABX-0036_NETRNA
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheFranceANR-15-CE11-0021-01
Russian Science FoundationRussian Federation16-14-10014
European Research Council294312
French National Research AgencyFranceFDT20140930867

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references, Other
  • Version 1.2: 2017-07-26
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-02-20
    Type: Advisory, Author supporting evidence, Data collection, Derived calculations