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- PDB-7oe1: 30S ribosomal subunit from E. coli -

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Basic information

Entry
Database: PDB / ID: 7oe1
Title30S ribosomal subunit from E. coli
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME / 30S subunit / RNA
Function / homology
Function and homology information


mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S17 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S21 / 30S ribosomal protein S2 / 30S ribosomal protein S14 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S17 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S21 / 30S ribosomal protein S2 / 30S ribosomal protein S14 / 30S ribosomal protein S11 / 30S ribosomal protein S9 / 30S ribosomal protein S18 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 30S ribosomal protein S10 / 30S ribosomal protein S16 / 30S ribosomal protein S3 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S19 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli str. K-12 substr. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsMaksimova, E. / Korepanov, A. / Baymukhametov, T. / Kravchenko, O. / Stolboushkina, E.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2021
Title: RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center.
Authors: Elena M Maksimova / Alexey P Korepanov / Olesya V Kravchenko / Timur N Baymukhametov / Alexander G Myasnikov / Konstantin S Vassilenko / Zhanna A Afonina / Elena A Stolboushkina /
Abstract: Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount ...Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an   strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: 16S rRNA
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6, fully modified isoform
H: 30S ribosomal protein S8
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
T: 30S ribosomal protein S20
B: 30S ribosomal protein S2
U: 30S ribosomal protein S21
C: 30S ribosomal protein S3
G: 30S ribosomal protein S7
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
S: 30S ribosomal protein S19


Theoretical massNumber of molelcules
Total (without water)787,56921
Polymers787,56921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area83710 Å2
ΔGint-668 kcal/mol
Surface area272980 Å2
MethodPISA

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA /


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules DEFHKLOPQRTBUCGIJMNS

#2: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XM56
#3: Protein 30S ribosomal protein S5 /


Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2YBZ5
#4: Protein 30S ribosomal protein S6, fully modified isoform / Ribosome


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P02358
#5: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XYQ3
#6: Protein 30S ribosomal protein S11 /


Mass: 13739.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpsK, FAZ83_23205
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2X4T2
#7: Protein 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A4S5B3M5
#8: Protein 30S ribosomal protein S15 /


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: C3SSQ8
#9: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XXS6
#10: Protein 30S ribosomal protein S17 /


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A4S5APA8
#11: Protein 30S ribosomal protein S18 /


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XHZ3
#12: Protein 30S ribosomal protein S20 /


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A4S5B3X7
#13: Protein 30S ribosomal protein S2 /


Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2W584
#14: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A5F1E8X4
#15: Protein 30S ribosomal protein S3 /


Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XYP0
#16: Protein 30S ribosomal protein S7 /


Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: C4ZUJ6
#17: Protein 30S ribosomal protein S9 /


Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XBM7
#18: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XQX6
#19: Protein 30S ribosomal protein S13 /


Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2XQ78
#20: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: A0A6D2WD65
#21: Protein 30S ribosomal protein S19 /


Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: E3PL00

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 30S ribosomal subunit from E.coli / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.85 MDa
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.14model fitting
13PHENIX1.18.2.-3874model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169371 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
14V4Q

4v4q

AA1
24V4Q

4v4q

AB1
34V4Q

4v4q

AC1
44V4Q

4v4q

AE1
54V4Q

4v4q

AF1
64V4Q

4v4q

AH1
74V4Q

4v4q

AI1
84V4Q

4v4q

AJ1
94V4Q

4v4q

AK1
104V4Q

4v4q

AG1
114V4Q

4v4q

AL1
124V4Q

4v4q

AM1
134V4Q

4v4q

AN1
144V4Q

4v4q

AO1
154V4Q

4v4q

AP1
164V4Q

4v4q

AQ1
174V4Q

4v4q

AR1
184V4Q

4v4q

AT1
194V4Q

4v4q

AU1
204V4Q

4v4q

AD1
214V4Q

4v4q

AS1

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