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- PDB-2r1c: Coordinates of the thermus thermophilus ribosome binding factor A... -

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Basic information

Entry
Database: PDB / ID: 2r1c
TitleCoordinates of the thermus thermophilus ribosome binding factor A (RbfA) homology model as fitted into the CRYO-EM map of a 30S-RBFA complex
ComponentsRibosome-binding factor A
KeywordsRNA BINDING PROTEIN / helix-kink-helix / KH domain / rRNA processing
Function / homologyRibosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / maturation of SSU-rRNA / K homology domain-like, alpha/beta / rRNA binding / cytoplasm / Ribosome-binding factor A
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsDatta, P.P. / Wilson, D.N. / Kawazoe, M. / Swami, N.K. / Kaminishi, T. / Sharma, M.R. / Booth, T.M. / Takemoto, C. / Fucini, P. / Yokoyama, S. / Agrawal, R.K.
CitationJournal: Mol Cell / Year: 2007
Title: Structural aspects of RbfA action during small ribosomal subunit assembly.
Authors: Partha P Datta / Daniel N Wilson / Masahito Kawazoe / Neil K Swami / Tatsuya Kaminishi / Manjuli R Sharma / Timothy M Booth / Chie Takemoto / Paola Fucini / Shigeyuki Yokoyama / Rajendra K Agrawal /
Abstract: Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ...Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 18, 2019Group: Data collection / Database references / Source and taxonomy
Category: database_2 / em_software / entity_src_gen
Item: _em_software.image_processing_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._em_software.image_processing_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Mar 13, 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 / 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

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Assembly

Deposited unit
A: Ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)10,8761
Polymers10,8761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ribosome-binding factor A / RbfA / TTHA0907


Mass: 10875.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0907 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SJV1

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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: THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH RBFA
Type: RIBOSOME / Details: RBFA WAS BOUND TO S1-DEPLETED 30S SUBUNIT
Buffer solutionName: 20mM, Hepes-KOH (pH 7.8), 10mM Mg(OAc)2, 200mM NH4Cl, 65mM KCl
pH: 7.8
Details: 20mM, Hepes-KOH (pH 7.8), 10mM Mg(OAc)2, 200mM NH4Cl, 65mM KCl
SpecimenConc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL HOLEY-CRBON FILM GRID
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: RAPID-FREEZING IN LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2005 / Details: ZEISS IMAGING SCANNER, STEP SIZE 14micro-m
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50760 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 131
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1Omodel fittingMANUAL
2SPIDER3D reconstruction
CTF correctionDetails: CTF CORRECTION OF 3D-MAPS BY WIENER FILTRATION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: REFERENCE BASED ALIGNMENT / Resolution: 12.5 Å / Num. of particles: 61207 / Actual pixel size: 2.76 Å / Magnification calibration: TMV
Details: CROSS-CORRELATION COEFFICIENT (CCF) VALUE FOR RBFA HOMOLOGY MODEL FITTED INTO THE CORRESPONDING CRYO-EM DENSITY WAS 0.79
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: X-RAY COORDINATES OF T. THERMOPHILUS 30S RIBOSOMAL SUBUNIT AND THE HOMOLOGY MODEL OF T. THERMOPHILUS RBFA WERE FITTED INTO THE 12.5 ANGSTROMS RESOLUTION CRYO-EM MAP OF THE T. ...Target criteria: X-RAY COORDINATES OF T. THERMOPHILUS 30S RIBOSOMAL SUBUNIT AND THE HOMOLOGY MODEL OF T. THERMOPHILUS RBFA WERE FITTED INTO THE 12.5 ANGSTROMS RESOLUTION CRYO-EM MAP OF THE T. THERMOPHILUS 30S SUBUNIT-RBFA COMPLEX. ALL THE ATOMIC COORDINATES WERE FITTED AS RIGID BODIES
Details: METHOD--CROSS-CORRELATION BASED MANUAL FITTING IN O REFINEMENT PROTOCOL--MULTIPLE RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11JOS

1jos

11JOS1PDBexperimental model
22DYJ

2dyj

12DYJ2PDBexperimental model
32R1G

2r1g

12R1G3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms736 0 0 0 736

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