6NQB

Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit


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 1.2 of the entry. See complete history

Literature

Role of Era in assembly and homeostasis of the ribosomal small subunit.

Razi, A.Davis, J.H.Hao, Y.Jahagirdar, D.Thurlow, B.Basu, K.Jain, N.Gomez-Blanco, J.Britton, R.A.Vargas, J.Guarne, A.Woodson, S.A.Williamson, J.R.Ortega, J.

(2019) Nucleic Acids Res. 47: 8301-8317

  • DOI: 10.1093/nar/gkz571

  • PubMed Abstract: 
  • Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly interm ...

    Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era's role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.


    Organizational Affiliation

    Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine,Houston, TX 77030, USA.,Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1 Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada.,Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
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: 2
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: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
99Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
74Escherichia coli H736Mutation(s): 0 
Gene Names: rpsS
Find proteins for F4SQ43 (Escherichia coli H736)
Go to UniProtKB:  F4SQ43
Entity ID: 6
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: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
93Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
129Escherichia coli (strain MS 21-1)Mutation(s): 0 
Gene Names: rpsH
Find proteins for D8A1L7 (Escherichia coli (strain MS 21-1))
Go to UniProtKB:  D8A1L7
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
123Escherichia coli 99.0741Mutation(s): 0 
Gene Names: rpsL
Find proteins for V6FZ95 (Escherichia coli 99.0741)
Go to UniProtKB:  V6FZ95
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN bS16
P
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
52Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsR
Find proteins for D7ZI16 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI16
Entity ID: 15
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: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
217Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 5
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNAA1542Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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

  • Deposited Date: 2019-01-20 
  • Released Date: 2019-06-26 
  • Deposition Author(s): Ortega, J.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaPJT-153044

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references
  • Version 1.2: 2019-09-18
    Type: Data collection, Database references