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- PDB-4wcw: Ribosomal silencing factor during starvation or stationary phase ... -

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Basic information

Entry
Database: PDB / ID: 4wcw
TitleRibosomal silencing factor during starvation or stationary phase (RsfS) from Mycobacterium tuberculosis
ComponentsRibosomal silencing factor RsfS
KeywordsTRANSLATION / Tuberculosis Ribosomal Silencing dimer / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / negative regulation of translation / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal silencing factor RsfS
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, X. / Sun, Q. / Jiang, C. / Yang, K. / Hung, L. / Zhang, J. / Sacchettini, J. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
CitationJournal: Structure / Year: 2015
Title: Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome.
Authors: Xiaojun Li / Qingan Sun / Cai Jiang / Kailu Yang / Li-Wei Hung / Junjie Zhang / James C Sacchettini /
Abstract: The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) ...The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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: Ribosomal silencing factor RsfS
D: Ribosomal silencing factor RsfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,49112
Polymers61,1084
Non-polymers3828
Water6,810378
1
A: Ribosomal silencing factor RsfS
B: Ribosomal silencing factor RsfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7456
Polymers30,5542
Non-polymers1914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint1 kcal/mol
Surface area11730 Å2
MethodPISA
2
C: Ribosomal silencing factor RsfS
D: Ribosomal silencing factor RsfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7456
Polymers30,5542
Non-polymers1914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-1 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.975, 50.975, 64.546
Angle α, β, γ (deg.)110.27, 96.17, 110.59
Int Tables number1
Space group name H-MP1
DetailsDimer confirmed by gel filtration

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Components

#1: Protein
Ribosomal silencing factor RsfS


Mass: 15277.115 Da / Num. of mol.: 4 / Mutation: Y102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: rsfS, Rv2420c, P425_02518, RVBD_2420c / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: O86327
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate pH6.5, 0.2 M Magnesium Acetate, 30% MPD

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.06 Å / Num. obs: 49832 / % possible obs: 93.3 % / Redundancy: 1.7 % / Net I/σ(I): 6.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O5A

2o5a


Resolution: 2.1→46.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1446 4.82 %
Rwork0.2105 --
obs0.2127 29976 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 22 378 3922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063590
X-RAY DIFFRACTIONf_angle_d0.8924870
X-RAY DIFFRACTIONf_dihedral_angle_d14.2851295
X-RAY DIFFRACTIONf_chiral_restr0.059559
X-RAY DIFFRACTIONf_plane_restr0.003652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.2881390.21892498X-RAY DIFFRACTION83
2.1751-2.26220.30621430.21512642X-RAY DIFFRACTION87
2.2622-2.36510.26481570.21642804X-RAY DIFFRACTION92
2.3651-2.48980.27211350.22292930X-RAY DIFFRACTION95
2.4898-2.64580.3131390.22712909X-RAY DIFFRACTION95
2.6458-2.850.26431400.22692987X-RAY DIFFRACTION96
2.85-3.13680.24591440.21732940X-RAY DIFFRACTION96
3.1368-3.59050.24591470.20252978X-RAY DIFFRACTION97
3.5905-4.52310.22521420.18422882X-RAY DIFFRACTION94
4.5231-46.07620.24021600.21332960X-RAY DIFFRACTION97

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