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- PDB-7afq: Ribosome binding factor A (RbfA) -

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Basic information

Entry
Database: PDB / ID: 7afq
TitleRibosome binding factor A (RbfA)
ComponentsRibosome-binding factor A
KeywordsRNA BINDING PROTEIN / Solution state NMR / 30S biogenesis / ribosome assembly / RbfA.
Function / homology
Function and homology information


ribosomal small subunit binding / response to cold / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / DNA damage response / cytoplasm / cytosol
Similarity search - Function
Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding factor A / 30S ribosome-binding factor
Similarity search - Component
Biological speciesEscherichia coli O26:H11 (bacteria)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsSchedlbauer, A. / Iturrioz, I. / Ochoa-Lizarralde, B. / Diercks, T. / Fucini, P. / Connell, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)CTQ2017-82222-R Spain
European CommissionPCIG14-GA-2013-632072 Spain
CitationJournal: Sci Adv / Year: 2021
Title: A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de ...Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de Astigarraga / David Gil-Carton / Paola Fucini / Sean R Connell /
Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high- ...While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
History
DepositionSep 19, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionDec 16, 2020ID: 6R8D
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Mar 17, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.id
Revision 1.3Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 8, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
V: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)15,1771
Polymers15,1771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6550 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribosome-binding factor A


Mass: 15176.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O26:H11 (bacteria) / Gene: rbfA, B9S25_002975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B7PAU8, UniProt: P0A7G2*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HNCA
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
161isotropic23D HN(CO)CA
1111isotropic23D HNCAHA
1101isotropic13D (H)CCH-TOCSY
191isotropic23D HN(CA)CO
181isotropic23D HNH NOESY
171isotropic23D CNH NOESY
1131isotropic23D HN(CO)CAHA
1121isotropic23D HCH NOESY

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Sample preparation

DetailsType: solution
Contents: 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP, 90% H2O/10% D2O
Label: sample 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMRbfA[U-13C; U-15N]1
10 mMHEPESnone1
6 mMMgCl2none1
30 mMNH4Clnone1
75 uMTCEPnone1
Sample conditionsIonic strength: 40 mM / Label: condition_1 / pH: 7.6 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
GROMACSEmile Apol, Rossen Apostolov, Paul Bauer, Herman J.C. Berendsen, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Rudi van Drunen, Anton Feenstra, Alan Gray, Gerrit Groenhof, Anca Hamuraru, Vincent Hindriksen M. Eric Irrgang, Aleksei Iupinov, Christoph Junghans, Joe Jordan, Dimitrios Karkoulis, Peter Kasson,, Jiri Kraus, Carsten Kutzner, Per Larsson, Justin A. Lemkul, Viveca Lindahl, Magnus Lundborg, Erik Marklund, Pascal Merz, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alexey Shvetsov, Alfons Sijbers, Peter Tieleman, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov.refinement
Refinement
MethodSoftware ordinal
simulated annealing5
molecular dynamics6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 60 / Conformers submitted total number: 20

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