6H4N

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 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

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.

Beckert, B.Turk, M.Czech, A.Berninghausen, O.Beckmann, R.Ignatova, Z.Plitzko, J.M.Wilson, D.N.

(2018) Nat Microbiol 3: 1115-1121

  • DOI: 10.1038/s41564-018-0237-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles <sup>1 </sup>. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation fac ...

    To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles 1 . In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF) 2-4 . Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria 5-8 , and reveals a unique role for bS1 in translation regulation.


    Organizational Affiliation

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany. plitzko@biochem.mpg.de.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany. Daniel.wilson@chemie.uni-hamburg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
218Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
157Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
161Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
98Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
116Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
88Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
143Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
93Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
50Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
66Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Ribosome modulation factor
v
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rmf
Find proteins for P0AFW2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFW2
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S1
y
557Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsA (ssyF)
Find proteins for P0AG67 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG67
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promoting factor
x
95Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hpf (yhbH)
Find proteins for P0AFX0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFX0
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1534Escherichia coli BW25113
Entity ID: 22
MoleculeChainsLengthOrganism
23S ribosomal RNAA2903Escherichia coli BW25113
Entity ID: 23
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli BW25113
Entity ID: 53
MoleculeChainsLengthOrganism
tRNAw77Escherichia coli BW25113
Entity ID: 57
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*UP*CP*CP*U)-3')I5Escherichia coli BW25113
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 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
GermanySPP1879
GermanyFOR1805

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Database references
  • Version 1.3: 2018-10-24
    Type: Advisory, Data collection, Derived calculations