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- PDB-1x1l: Interaction of ERA,a GTPase protein, with the 3'minor domain of t... -

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Basic information

Entry
Database: PDB / ID: 1x1l
TitleInteraction of ERA,a GTPase protein, with the 3'minor domain of the 16S rRNA within the THERMUS THERMOPHILUS 30S subunit.
Components
  • GTP-binding protein era
  • RNA (130-MER)
KeywordsSTRUCTURAL PROTEIN/RNA / Interaction of Era protein with the 3'minor domain of 16S rRNA / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


guanosine tetraphosphate binding / ribosomal small subunit binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / protein phosphorylation / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / ribosomal small subunit binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / protein phosphorylation / GTPase activity / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / GTPase Era
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsSharma, M.R. / Barat, C. / Agrawal, R.K.
Citation
Journal: Mol Cell / Year: 2005
Title: Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly.
Authors: Manjuli R Sharma / Chandana Barat / Daniel N Wilson / Timothy M Booth / Masahito Kawazoe / Chie Hori-Takemoto / Mikako Shirouzu / Shigeyuki Yokoyama / Paola Fucini / Rajendra K Agrawal /
Abstract: Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to ...Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to accumulation of an unprocessed precursor of the 16S rRNA. We have obtained a three-dimensional cryo-electron microscopic map of the Thermus thermophilus 30S-Era complex. Era binds in the cleft between the head and platform of the 30S subunit and locks the subunit in a conformation that is not favorable for association with the large (50S) ribosomal subunit. The RNA binding KH motif present within the C-terminal domain of Era interacts with the conserved nucleotides in the 3' region of the 16S rRNA. Furthermore, Era makes contact with several assembly elements of the 30S subunit. These observations suggest a direct involvement of Era in the assembly and maturation of the 30S subunit.
#1: Journal: Nature / Year: 2000
Title: Molecular biology. Small subunit, big science.
#2: Journal: Proc Natl Acad Sci U S A / Year: 1999
Title: Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif.
Authors: X Chen / D L Court / X Ji /
Abstract: ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in ...ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in eukaryotes. Here we report the crystal structure of ERA from Escherichia coli. The structure has been determined at 2.4-A resolution. It reveals a two-domain arrangement of the molecule: an N-terminal domain that resembles p21 Ras and a C-terminal domain that is unique. Structure-based topological search of the C domain fails to reveal any meaningful match, although sequence analysis suggests that it contains a KH domain. KH domains are RNA binding motifs that usually occur in tandem repeats and exhibit low sequence similarity except for the well-conserved segment VIGxxGxxIK. We have identified a betaalphaalphabeta fold that contains the VIGxxGxxIK sequence and is shared by the C domain of ERA and the KH domain. We propose that this betaalphaalphabeta fold is the RNA binding motif, the minimum structural requirement for RNA binding. ERA dimerizes in crystal. The dimer formation involves a significantly distorted switch II region, which may shed light on how ERA protein regulates downstream events.
#3: Journal: To be Published
Title: Crystal structure of Era from Thermus thermophilus
Authors: Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Sekine, S. / Shirouzu, M. / Fucini, P. / Agrawal, R.K. / Yokoyama, S.
History
DepositionApr 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Category: database_2 / em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Mar 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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Structure visualization

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Assembly

Deposited unit
A: RNA (130-MER)
X: GTP-binding protein era


Theoretical massNumber of molelcules
Total (without water)76,1612
Polymers76,1612
Non-polymers00
Water0
1


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

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Components

#1: RNA chain RNA (130-MER) / Coordinate model: P atoms only


Mass: 42303.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#2: Protein GTP-binding protein era / Coordinate model: Cα atoms only


Mass: 33858.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06616

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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 Era
Type: RIBOSOME / Details: Era was bound to a S1-depleted 30S subunit
Buffer solutionName: Hepes-KOH / pH: 7.5 / Details: Hepes-KOH
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holley-carbon film GRIDS
VitrificationDetails: 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: Mar 25, 2003
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: 49696 X / Nominal defocus max: 3940 nm / Nominal defocus min: 1180 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
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: 13.5 Å / Actual pixel size: 2.82 Å / Magnification calibration: TMV
Details: projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure. The number of missing atoms was so much ...Details: projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in rRNA are present in the structure. The number of missing atoms was so much that remark 470 for the missing atoms list were removed.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: X-ray coordinates of the 30S ribosomal subunit and ERA were fitted into the 13.5 angstroms resolution CRYO-EM map of the T. Thermophilus 30S subunit-ERA complex. the atomic structure ...Target criteria: X-ray coordinates of the 30S ribosomal subunit and ERA were fitted into the 13.5 angstroms resolution CRYO-EM map of the T. Thermophilus 30S subunit-ERA complex. the atomic structure of ERA was fitted as 3 rigid bodies, N-terminal domain, C-terminal domain and C-terminal helix within the C-terminal domain. The resultant ERA structure was then energy minimized. The X-ray coordinates of T. Thermophilus 30S subunit was fitted as 4 rigid bodies, head, body, platform and 16S rRNA 3' minor domains. Only the coordinates of the 16S rRNA 3' minor domain and ERA are included HERE. The KH domain of ERA makes direct contact with the 3' terminus of the 16S rRNA.
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
11FJF

1fjf
PDB Unreleased entry

11FJF1PDBexperimental model
21EGA11EGA2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms292 130 0 0 422

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