5NO3

RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate without uS3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.16 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

RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket.

Lopez-Alonso, J.P.Kaminishi, T.Kikuchi, T.Hirata, Y.Iturrioz, I.Dhimole, N.Schedlbauer, A.Hase, Y.Goto, S.Kurita, D.Muto, A.Zhou, S.Naoe, C.Mills, D.J.Gil-Carton, D.Takemoto, C.Himeno, H.Fucini, P.Connell, S.R.

(2017) Nucleic Acids Res 45: 6945-6959

  • DOI: 10.1093/nar/gkx324
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly ...

    During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.


    Organizational Affiliation

    IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
224Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Small ribosomal subunit biogenesis GTPase RsgA
Z
313Escherichia coli K-12Mutation(s): 0 
Gene Names: rsgAengCyjeQb4161JW4122
EC: 3.6.1
Find proteins for P39286 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
14Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
106Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1534Escherichia coli K-12
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
Z
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B, Z
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, N, P, T, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-09-13
    Changes: Database references