5NO2

RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate)


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
  • Primary Citation of Related Structures:  
    5NO3, 5NO2, 5NO4

  • 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 LengthOrganismDetailsImage
30S ribosomal protein S4D205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F106Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L14Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14N100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Small ribosomal subunit biogenesis GTPase RsgAZ313Escherichia coli K-12Mutation(s): 0 
Gene Names: rsgAengCyjeQb4161JW4122
EC: 3.6.1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
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

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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: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-09-13
    Changes: Database references