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- PDB-8bxa: Crystal structure of ribosome binding factor A (RbfA) from S. aureus -

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Basic information

Entry
Database: PDB / ID: 8bxa
TitleCrystal structure of ribosome binding factor A (RbfA) from S. aureus
ComponentsRibosome-binding factor A
KeywordsRIBOSOME / maturation / 30S subunit / S. aureus
Function / homology
Function and homology information


ribosomal small subunit binding / maturation of SSU-rRNA / ribosome biogenesis / 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 domain-like, alpha/beta
Similarity search - Domain/homology
Ribosome-binding factor A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsFatkhullin, B. / Bikmullin, A. / Gabdulkhakov, A. / Khusainov, I. / Validov, S. / Usachev, K. / Yusupov, M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-54-15001 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from .
Authors: Aydar G Bikmullin / Bulat Fatkhullin / Artem Stetsenko / Azat Gabdulkhakov / Natalia Garaeva / Liliia Nurullina / Evelina Klochkova / Alexander Golubev / Iskander Khusainov / Natalie ...Authors: Aydar G Bikmullin / Bulat Fatkhullin / Artem Stetsenko / Azat Gabdulkhakov / Natalia Garaeva / Liliia Nurullina / Evelina Klochkova / Alexander Golubev / Iskander Khusainov / Natalie Trachtmann / Dmitriy Blokhin / Albert Guskov / Shamil Validov / Konstantin Usachev / Marat Yusupov /
Abstract: Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and ...Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins' folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S-RbfA complex from (). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.
History
DepositionDec 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)13,5361
Polymers13,5361
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.315, 65.315, 27.287
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Ribosome-binding factor A


Mass: 13535.722 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: rbfA, SAOUHSC_01247 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G2Q4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 80 mM Manganese(II) chloride, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.991872 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991872 Å / Relative weight: 1
ReflectionResolution: 2.22→46.18 Å / Num. obs: 5910 / % possible obs: 99.88 % / Redundancy: 7.2 % / Biso Wilson estimate: 49.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0585 / Rpim(I) all: 0.0233 / Rrim(I) all: 0.06307 / Net I/σ(I): 18.6
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7828 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 592 / CC1/2: 0.893 / Rpim(I) all: 0.3197 / Rrim(I) all: 0.8472 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→46.18 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.5798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 296 5.01 %
Rwork0.1985 5613 -
obs0.201 5909 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.79 Å2
Refinement stepCycle: LAST / Resolution: 2.22→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 0 0 14 807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092848
X-RAY DIFFRACTIONf_angle_d1.00581137
X-RAY DIFFRACTIONf_chiral_restr0.0534130
X-RAY DIFFRACTIONf_plane_restr0.0054147
X-RAY DIFFRACTIONf_dihedral_angle_d16.3141343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.80.32971450.25162757X-RAY DIFFRACTION99.9
2.8-46.180.22871510.18652856X-RAY DIFFRACTION99.93

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