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- PDB-6sj5: Crystal structure of the uL14-RsfS complex from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6sj5
TitleCrystal structure of the uL14-RsfS complex from Staphylococcus aureus
Components
  • 50S ribosomal protein L14
  • Ribosomal silencing factor RsfS
KeywordsRIBOSOME / Stress / S.aureus / RsfS / Hibernation
Function / homology
Function and homology information


negative regulation of ribosome biogenesis / cytosolic ribosome assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / structural constituent of ribosome / translation / cytoplasm
Similarity search - Function
Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Ribosomal protein L14P, bacterial-type / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. ...Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Ribosomal protein L14P, bacterial-type / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / PHOSPHATE ION / Ribosomal silencing factor RsfS / Large ribosomal subunit protein uL14 / Ribosomal silencing factor RsfS
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26686551714 Å
AuthorsFatkhullin, B. / Gabdulkhakov, A. / Yusupova, G. / Yusupov, M.
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.
Authors: Iskander Khusainov / Bulat Fatkhullin / Simone Pellegrino / Aydar Bikmullin / Wen-Ti Liu / Azat Gabdulkhakov / Amr Al Shebel / Alexander Golubev / Denis Zeyer / Natalie Trachtmann / Georg A ...Authors: Iskander Khusainov / Bulat Fatkhullin / Simone Pellegrino / Aydar Bikmullin / Wen-Ti Liu / Azat Gabdulkhakov / Amr Al Shebel / Alexander Golubev / Denis Zeyer / Natalie Trachtmann / Georg A Sprenger / Shamil Validov / Konstantin Usachev / Gulnara Yusupova / Marat Yusupov /
Abstract: For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced ...For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced proteins to the ribosome to prevent unnecessary translation. One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 protein onto the large ribosomal subunit and prevents its association with the small subunit. Here we describe the binding mode of Staphylococcus aureus RsfS to the large ribosomal subunit and present a 3.2 Å resolution cryo-EM reconstruction of the 50S-RsfS complex together with the crystal structure of uL14-RsfS complex solved at 2.3 Å resolution. The understanding of the detailed landscape of RsfS-uL14 interactions within the ribosome shed light on the mechanism of ribosome shutdown in the human pathogen S. aureus and might deliver a novel target for pharmacological drug development and treatment of bacterial infections.
History
DepositionAug 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal silencing factor RsfS
B: Ribosomal silencing factor RsfS
C: 50S ribosomal protein L14
D: 50S ribosomal protein L14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9279
Polymers57,5924
Non-polymers3355
Water28816
1
A: Ribosomal silencing factor RsfS
C: 50S ribosomal protein L14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0716
Polymers28,7962
Non-polymers2754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-10 kcal/mol
Surface area11360 Å2
MethodPISA
2
B: Ribosomal silencing factor RsfS
D: 50S ribosomal protein L14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8563
Polymers28,7962
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-6 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.107, 117.601, 121.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ribosomal silencing factor RsfS


Mass: 13467.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: rsfS, E5491_08675, FAF14_04505, FAF30_12305, FAF31_00945, FAF32_10770, QU38_08975
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D1JM30, UniProt: W8TVV3*PLUS
#2: Protein 50S ribosomal protein L14


Mass: 15328.716 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: rplN, SAOUHSC_02502 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FW16
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Lithium sulfate, 0.1 M MES pH 6.0, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.267→42.29 Å / Num. obs: 25254 / % possible obs: 98.95 % / Redundancy: 4.48 % / Biso Wilson estimate: 69.5777354322 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.53
Reflection shellResolution: 2.267→2.348 Å / Redundancy: 4.39 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2494 / CC1/2: 0.273 / % possible all: 99.17

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O5A, 5ND8

2o5a

5nd8


Resolution: 2.26686551714→42.2029407831 Å / SU ML: 0.390702518887 / Cross valid method: FREE R-VALUE / σ(F): 1.35468090639 / Phase error: 32.7644601701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263589906064 1262 4.99861369668 %
Rwork0.228546353822 23985 -
obs0.230306473507 25247 98.9496374682 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.2172954769 Å2
Refinement stepCycle: LAST / Resolution: 2.26686551714→42.2029407831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 21 16 3709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023951684463729
X-RAY DIFFRACTIONf_angle_d1.13384391945019
X-RAY DIFFRACTIONf_chiral_restr0.0657136377329574
X-RAY DIFFRACTIONf_plane_restr0.00558938311432659
X-RAY DIFFRACTIONf_dihedral_angle_d16.29224401411419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2669-2.35760.3803585064491370.3497081720892610X-RAY DIFFRACTION99.0623873062
2.3576-2.46490.3495654089721400.3399027648292647X-RAY DIFFRACTION99.7137745975
2.4649-2.59480.3615399643241370.3330911780412614X-RAY DIFFRACTION99.4577006508
2.5948-2.75740.3414889195731390.3211887272142634X-RAY DIFFRACTION99.283924096
2.7574-2.97020.3895131291131400.3045552772532656X-RAY DIFFRACTION99.6081225508
2.9702-3.2690.3544769169871400.2804965719332662X-RAY DIFFRACTION99.1507430998
3.269-3.74180.2445123600651410.2384462198412678X-RAY DIFFRACTION98.6354093772
3.7418-4.71330.2452163749771410.1985311677552685X-RAY DIFFRACTION98.6387434555
4.7133-42.2020.2193428180441470.1892253059072799X-RAY DIFFRACTION97.2598217233
Refinement TLS params.Method: refined / Origin x: 5.82612513189 Å / Origin y: 3.81488691363 Å / Origin z: 13.3497025537 Å
111213212223313233
T0.328067340079 Å2-0.074407441328 Å20.108381366374 Å2-0.338572650169 Å2-0.00468102083328 Å2--0.331499833625 Å2
L0.121392050125 °20.113084684864 °20.384783821873 °2-0.517767617931 °20.28532106935 °2--0.088279526155 °2
S-0.0501000246264 Å °0.163114413687 Å °0.0815842443611 Å °0.132814350446 Å °-0.0596947515702 Å °0.0502074797044 Å °0.124758500338 Å °0.0391219990662 Å °1.26140869245E-10 Å °
Refinement TLS groupSelection details: all

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