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Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.

Beckert, B.Abdelshahid, M.Schafer, H.Steinchen, W.Arenz, S.Berninghausen, O.Beckmann, R.Bange, G.Turgay, K.Wilson, D.N.

(2017) EMBO J. 36: 2061-2072

  • DOI: 10.15252/embj.201696189

  • PubMed Abstract: 
  • Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In Escherichia coli, dimerization of 70S ribosomes into 100S requires the action of ...

    Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In Escherichia coli, dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of E. coli 100S (Ec100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the Bacillus subtilis hibernating 100S (Bs100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the BsHPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as E. coli.


    Organizational Affiliation

    Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
224Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P21464 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21464
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
210Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P21465 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21465
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
199Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsD
Find proteins for P21466 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21466
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
165Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsE (spcA)
Find proteins for P21467 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21467
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P21468 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21468
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
153Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P21469 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21469
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
131Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P12879 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12879
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
130Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P21470 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21470
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
102Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsJ (tetA)
Find proteins for P21471 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21471
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
118Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P04969 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P04969
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
137Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsL (fun, strA)
Find proteins for P21472 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21472
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
111Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P20282 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20282
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
60Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsN1 (rpsN, rpsNA, rpsZ)
Find proteins for P12878 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12878
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
88Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsO
Find proteins for P21473 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21473
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
89Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P21474 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21474
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
86Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P12874 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12874
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
71Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P21475 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21475
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
80Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P21476 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21476
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
86Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpsT (yqeO)
Find proteins for P21477 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P21477
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
W
275Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplB
Find proteins for P42919 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42919
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
X
207Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplC
Find proteins for P42920 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42920
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
Y
205Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplD
Find proteins for P42921 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42921
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
Z
178Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplE
Find proteins for P12877 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12877
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
a
175Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplF
Find proteins for P46898 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46898
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
b
123Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P42923 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42923
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
c
142Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplM
Find proteins for P70974 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P70974
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
d
122Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplN
Find proteins for P12875 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12875
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
e
146Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplO
Find proteins for P19946 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19946
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
f
138Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplP
Find proteins for P14577 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P14577
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
g
119Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P20277 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20277
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
h
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplR
Find proteins for P46899 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46899
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
i
114Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplS
Find proteins for O31742 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31742
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
j
117Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplT
Find proteins for P55873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55873
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
k
101Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplU
Find proteins for P26908 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P26908
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
l
109Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplV
Find proteins for P42060 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42060
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
m
93Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplW
Find proteins for P42924 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42924
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
n
100Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplX
Find proteins for P0CI78 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P0CI78
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
o
82Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P05657 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05657
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
p
54Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmF
Find proteins for O34687 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34687
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 1
q
48Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmGA (rpmG1)
Find proteins for P56849 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P56849
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
r
44Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmH
Find proteins for P05647 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05647
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
s
64Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P55874 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55874
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
t
36Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P20278 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20278
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
u
58Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmB (yloT)
Find proteins for P37807 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37807
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
v
65Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P12873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12873
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
w
58Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P19947 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19947
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
y
64Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q03223 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q03223
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
x
104Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yvyD (hpf, yviI)
Find proteins for P28368 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P28368
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1544Bacillus subtilis subsp. subtilis str. 168
Entity ID: 21
MoleculeChainsLengthOrganism
23S ribosomal RNAU2923Bacillus subtilis subsp. subtilis str. 168
Entity ID: 22
MoleculeChainsLengthOrganism
5S ribosomal RNAV112Bacillus subtilis subsp. subtilis str. 168
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP-1879

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Structure summary
  • Version 1.2: 2017-07-26
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-02-20
    Type: Advisory, Data collection, Derived calculations