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- PDB-2r1g: Coordinates of the thermus thermophilus 30S components neighborin... -

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Basic information

Entry
Database: PDB / ID: 2r1g
TitleCoordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex
Components
  • (16S RIBOSOMAL RNA HELIX ...) x 7
  • (30S ribosomal protein ...) x 3
KeywordsRIBOSOMAL PROTEIN/RNA / 30S RIBOSOME MATURATION PROTEIN RbfA / COLD SHOCK RESPONSE PROTEIN RbfA / 30S-RbfA COMPLEX / RbfA BINDING SITE ON THE 30S / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Antibiotic resistance / RIBOSOMAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / cytoplasm
Similarity search - Function
Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S9, conserved site / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. ...Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S9, conserved site / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S9 signature. / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
synthetic construct (others)
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.
Citation
Journal: 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.
#1: Journal: Nature / Year: 2000
Title: Molecular biology. Small subunit, big science.
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 / pdbx_entity_src_syn / Item: _em_software.image_processing_id
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: 16S RIBOSOMAL RNA HELIX 1
B: 16S RIBOSOMAL RNA HELIX 18
C: 16S RIBOSOMAL RNA HELIX 27
D: 16S RIBOSOMAL RNA HELIX 28
E: 16S RIBOSOMAL RNA HELIX 44
X: 16S RIBOSOMAL RNA HELIX 44
F: 16S RIBOSOMAL RNA HELIX 45
G: 30S ribosomal protein S9
H: 30S ribosomal protein S12
I: 30S ribosomal protein S13


Theoretical massNumber of molelcules
Total (without water)100,46910
Polymers100,46910
Non-polymers00
Water0
1


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

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Components

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16S RIBOSOMAL RNA HELIX ... , 7 types, 7 molecules ABCDEXF

#1: RNA chain 16S RIBOSOMAL RNA HELIX 1 / Coordinate model: P atoms only


Mass: 7781.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain 16S RIBOSOMAL RNA HELIX 18 / Coordinate model: P atoms only


Mass: 15544.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain 16S RIBOSOMAL RNA HELIX 27 / Coordinate model: P atoms only


Mass: 9440.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain 16S RIBOSOMAL RNA HELIX 28 / Coordinate model: P atoms only


Mass: 8969.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: RNA chain 16S RIBOSOMAL RNA HELIX 44 / Coordinate model: P atoms only


Mass: 3457.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: RNA chain 16S RIBOSOMAL RNA HELIX 44 / Coordinate model: P atoms only


Mass: 3530.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: RNA chain 16S RIBOSOMAL RNA HELIX 45 / Coordinate model: P atoms only


Mass: 9434.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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30S ribosomal protein ... , 3 types, 3 molecules GHI

#8: Protein 30S ribosomal protein S9 / / Coordinate model: Cα atoms only


Mass: 14298.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: rpsI, rps9 / Production host: Escherichia coli (E. coli) / References: UniProt: P62669
#9: Protein 30S ribosomal protein S12 / / Coordinate model: Cα atoms only


Mass: 13804.311 Da / Num. of mol.: 1 / Fragment: residues 5-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: rpsL, rps12 / Production host: Escherichia coli (E. coli) / References: UniProt: P17293, UniProt: P61941*PLUS
#10: Protein 30S ribosomal protein S13 / / Coordinate model: Cα atoms only


Mass: 14207.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: rpsM, rps13 / Production host: Escherichia coli (E. coli) / References: UniProt: P62655

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Details

Sequence detailsSICNE THE PORTION (1411-1489) OF H44 IS NOT CLOSE TO THE RBFA, THE AUTHOR DID NOT PROVIDE THOSE ...SICNE THE PORTION (1411-1489) OF H44 IS NOT CLOSE TO THE RBFA, THE AUTHOR DID NOT PROVIDE THOSE COORDINATES. THE AUTHOR ONLY PROVIDED THE COORDINATES OF THE PORTION OF THE H44 (CHAINS E AND X) THAT IS CLOSE TO THE RBFA.

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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 18, 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 FIELDBright-field microscopy / 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: CRYO-ELECTRON MICROSCOPY AND 3D IMAGE PROCESSING / Resolution: 12.5 Å / Num. of particles: 61207 / Actual pixel size: 2.76 Å / Magnification calibration: TMV
Details: This entry contains only a CA trace for the protein and only phosphorus atom for the RNA in the coordinate. CROSS-CORRELATION COEFFICIENT (CCF) VALUE FOR RBFA HOMOLOGY MODEL FITTED INTO THE ...Details: This entry contains only a CA trace for the protein and only phosphorus atom for the RNA in the coordinate. 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 buildingPDB-ID: 1J5E

1j5e


Accession code: 1J5E / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms376 180 0 0 556

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