5MYJ

Structure of 70S ribosome from Lactococcus lactis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.

Franken, L.E.Oostergetel, G.T.Pijning, T.Puri, P.Arkhipova, V.Boekema, E.J.Poolman, B.Guskov, A.

(2017) Nat Commun 8: 722-722

  • DOI: 10.1038/s41467-017-00718-x

  • PubMed Abstract: 
  • Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we re ...

    Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPFlong. The N-terminal domain of HPFlong binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPFlong binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPFlong, and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPFlong due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPFlong-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.


    Organizational Affiliation

    Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
255Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsB
Find proteins for A2RNV0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNV0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
217Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsC
Find proteins for A2RNP9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
203Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsD
Find proteins for A2RI10 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RI10
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
168Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsE
Find proteins for A2RNN6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
97Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsF
Find proteins for A2RNZ4 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNZ4
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
155Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsG
Find proteins for A2RP73 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RP73
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
132Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsH
Find proteins for A2RNN9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
130Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsI
Find proteins for A2RP61 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RP61
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
102Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for A2RNQ6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ6
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
127Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsK
Find proteins for A2RNM8 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNM8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
137Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsL
Find proteins for A2RP74 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RP74
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
121Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsM
Find proteins for A2RNM9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNM9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN
61Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A2RNP2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
89Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsO
Find proteins for A2RMV9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RMV9
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
90Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsP
Find proteins for A2RJS1 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RJS1
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
86Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for A2RNP6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
81Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsR
Find proteins for A2RNZ2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNZ2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
92Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsS
Find proteins for A2RNQ1 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ1
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
77Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsT
Find proteins for A2RMG0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RMG0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
58Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpsU
Find proteins for A2RHW9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RHW9
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B0
64Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmB
Find proteins for A2RHS3 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RHS3
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B1
69Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmC
Find proteins for A2RNP7 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP7
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B2
59Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmD
Find proteins for A2RNN5 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN5
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
B3
81Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmE2
Find proteins for A2RJP7 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RJP7
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B4
57Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmF
Find proteins for A2RHH0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RHH0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 3
B5
49Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmG3 (rpmGC)
Find proteins for A2RNR2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNR2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B6
44Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmH
Find proteins for A2RHL6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RHL6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B7
66Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmI
Find proteins for A2RMR2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RMR2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B8
38Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A2RNN0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN0
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD
276Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplB
Find proteins for A2RNQ2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ2
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE
207Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplC
Find proteins for A2RNQ5 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ5
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF
208Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplD
Find proteins for A2RNQ4 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ4
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG
180Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplE
Find proteins for A2RNP3 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP3
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH
178Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplF
Find proteins for A2RNN8 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN8
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BM
148Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplM
Find proteins for A2RP62 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RP62
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BN
122Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplN
Find proteins for A2RNP5 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP5
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BO
147Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplO
Find proteins for A2RNN4 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN4
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BP
137Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplP
Find proteins for A2RNP8 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BQ
126Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplQ
Find proteins for A2RNM6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNM6
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BR
115Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplR
Find proteins for A2RNN7 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN7
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BS
114Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplS
Find proteins for A2RLS5 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RLS5
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BT
119Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplT
Find proteins for A2RMR1 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RMR1
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BU
104Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplU
Find proteins for A2RLA4 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RLA4
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BV
115Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplV
Find proteins for A2RNQ0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ0
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BW
97Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplW
Find proteins for A2RNQ3 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ3
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BX
101Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rplX
Find proteins for A2RNP4 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP4
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BZ
94Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: rpmA
Find proteins for A2RLA2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RLA2
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
A
185Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: hpf (yfiA)
Find proteins for A2RIX0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RIX0
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1535Lactococcus lactis subsp. cremoris MG1363
Entity ID: 31
MoleculeChainsLengthOrganism
23S ribosomal RNABA2897Lactococcus lactis subsp. cremoris MG1363
Entity ID: 32
MoleculeChainsLengthOrganism
5S ribosomal RNABB115Lactococcus lactis subsp. cremoris MG1363
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.6 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
NWONetherlandsTOPGO L.10.060
European Research CouncilNetherlandsERC-2014-ADG

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release