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 1.3 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: https://doi.org/10.1093/nar/gkx324
  • Primary Citation of Related Structures:  
    5NO2, 5NO3, 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 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

    Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4B [auth D]205Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5C [auth E]155Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6D [auth F]106Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7E [auth G]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8F [auth H]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9G [auth I]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10H [auth J]99Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11I [auth K]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12J [auth L]14Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13K [auth M]114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14L [auth N]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15M [auth O]88Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16N [auth P]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17O [auth Q]80Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18P [auth R]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19Q [auth S]79Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20R [auth T]86Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit biogenesis GTPase RsgAS [auth Z]313Escherichia coli K-12Mutation(s): 0 
Gene Names: rsgAengCyjeQb4161JW4122
EC: 3.6.1
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,534Escherichia coli K-12
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
MC [auth Z]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
LC [auth Z]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
BA [auth A]
BB [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
IA [auth A],
IB [auth A],
IC [auth N],
JA [auth A],
JB [auth A],
JC [auth P],
KA [auth A],
KB [auth A],
KC [auth T],
LA [auth A],
LB [auth A],
MA [auth A],
MB [auth A],
NA [auth A],
NB [auth A],
NC [auth Z],
OA [auth A],
OB [auth A],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
T [auth A],
TA [auth A],
TB [auth A],
U [auth A],
UA [auth A],
UB [auth A],
V [auth A],
VA [auth A],
VB [auth A],
W [auth A],
WA [auth A],
WB [auth A],
X [auth A],
XA [auth A],
XB [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIXdev-2621-000
MODEL REFINEMENTREFMAC5.8.0155

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-04-24
    Changes: Data collection, Database references, Derived calculations