5UZ4

The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 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

The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.

Razi, A.Guarne, A.Ortega, J.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E3396-E3403

  • DOI: 10.1073/pnas.1618016114

  • PubMed Abstract: 
  • Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechan ...

    Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit.


    Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8S4K1.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
131Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsH
Find proteins for B7MCS1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsI
Find proteins for B7MBZ1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBZ1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
129Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsK
Find proteins for B7MCR3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
124Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsL
Find proteins for B7MCV7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 13
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: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
89Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 15
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: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
84Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for B7MCS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
75Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsR
Find proteins for B7MLK7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MLK7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Small ribosomal subunit biogenesis GTPase RsgA
Z
334Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rsgA (engC, yjeQ)
EC: 3.6.1.-
Find proteins for P39286 (Escherichia coli (strain K12))
Go to UniProtKB:  P39286
Entity ID: 1
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNAA1527Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
Z
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GGM
Query on GGM

Download SDF File 
Download CCD File 
Z
3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-triphosphate
MANT-GMPPNP
C18 H24 N7 O14 P3
ZGTKZICAFACDSP-XNIJJKJLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 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
Canadian Institutes of Health ResearchCanadaMOP-82930

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references
  • Version 1.2: 2017-05-10
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Data collection