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- PDB-7oi0: E.coli delta rbfA pre-30S ribosomal subunit class D -

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Basic information

Entry
Database: PDB / ID: 7oi0
TitleE.coli delta rbfA pre-30S ribosomal subunit class D
Components
  • (30S ribosomal protein ...) x 10
  • 16S rRNA
KeywordsRIBOSOME / 30S subunit / RNA / RBFA
Function / homology
Function and homology information


mRNA 5'-UTR binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation ...mRNA 5'-UTR binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 ...Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / 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 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 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / S4 RNA-binding domain / Ribosomal protein S11 / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S17 / 30S ribosomal protein S15 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S11 / 30S ribosomal protein S18 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S17 / 30S ribosomal protein S15 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S11 / 30S ribosomal protein S18 / 30S ribosomal protein S4 / 30S ribosomal protein S16 / 30S ribosomal protein S8 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 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
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-12916
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
D: 30S ribosomal protein S4
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
A: 16S rRNA


Theoretical massNumber of molelcules
Total (without water)627,76511
Polymers627,76511
Non-polymers00
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36400 Å2
ΔGint-328 kcal/mol
Surface area160780 Å2
MethodPISA

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Components

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30S ribosomal protein ... , 10 types, 10 molecules DFHKLOPQRT

#1: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A6D2XM56
#2: Protein 30S ribosomal protein S6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358
#3: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A6D2XYQ3
#4: Protein 30S ribosomal protein S11


Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A6D2X4T2
#5: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A4S5B3M5
#6: Protein 30S ribosomal protein S15


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A4S5B232
#7: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A6D2XXS6
#8: Protein 30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A4S5APA8
#9: Protein 30S ribosomal protein S18


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A6D2XHZ3
#10: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A4S5B3X7

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RNA chain / Non-polymers , 2 types, 375 molecules A

#11: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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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: E. coli pre-30S delta rbfA ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#11 / Source: NATURAL
Molecular weightValue: 0.85 MDa
Source (natural)Organism: Escherichia coli BW25113 (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 FIELD
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106319 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 4V4Q / Initial refinement model-ID: 1 / PDB-ID: 4V4Q

4v4q

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1AA
2

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