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- PDB-1x18: Contact sites of ERA GTPase on the THERMUS THERMOPHILUS 30S SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1x18
TitleContact sites of ERA GTPase on the THERMUS THERMOPHILUS 30S SUBUNIT
Components
  • (30S ribosomal protein ...) x 4
  • 5'-R(P*CP*GP*AP*UP*GP*GP*CP*GP*AP*AP*G)-3'
  • 5'-R(P*UP*GP*UP*UP*GP*GP*GP*UP*UP*AP*AP*GP*UP*CP*CP*CP*GP*CP*AP*AP*CP*GP*AP*G)-3'
  • 5'-R(P*UP*UP*CP*CP*CP*GP*GP*GP*CP*CP*UP*GP*GP*GP*GP*CP*CP*CP*GP*C)-3'
  • GTP-binding protein era
  • RNA (31-MER)
KeywordsSTRUCTURAL PROTEIN/RNA / Contact sites of Era protein on the 30S ribosomal subunit / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S2 signature 1. ...Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal S11, conserved site / Ribosomal protein S7p/S5e / Ribosomal protein S11 / Ribosomal protein S11 / Ribosomal protein S11 signature. / Ribosomal protein S11 superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
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: Structure of the 30S ribosomal subunit.
Authors: B T Wimberly / D E Brodersen / W M Clemons / R J Morgan-Warren / A P Carter / C Vonrhein / T Hartsch / V Ramakrishnan /
Abstract: Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we ...Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.
#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 2, 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, 2013Group: Structure summary
Revision 1.4Dec 18, 2019Group: Data collection / Database references / Category: database_2 / em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.5Mar 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: 5'-R(P*CP*GP*AP*UP*GP*GP*CP*GP*AP*AP*G)-3'
B: RNA (31-MER)
C: 5'-R(P*UP*UP*CP*CP*CP*GP*GP*GP*CP*CP*UP*GP*GP*GP*GP*CP*CP*CP*GP*C)-3'
D: 5'-R(P*UP*GP*UP*UP*GP*GP*GP*UP*UP*AP*AP*GP*UP*CP*CP*CP*GP*CP*AP*AP*CP*GP*AP*G)-3'
E: 30S ribosomal protein S2
F: 30S ribosomal protein S7
G: 30S ribosomal protein S11
H: 30S ribosomal protein S18
X: GTP-binding protein era


Theoretical massNumber of molelcules
Total (without water)126,1169
Polymers126,1169
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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RNA chain , 4 types, 4 molecules ABCD

#1: RNA chain 5'-R(P*CP*GP*AP*UP*GP*GP*CP*GP*AP*AP*G)-3' / Coordinate model: P atoms only


Mass: 3585.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#2: RNA chain RNA (31-MER) / Coordinate model: P atoms only


Mass: 9974.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#3: RNA chain 5'-R(P*UP*UP*CP*CP*CP*GP*GP*GP*CP*CP*UP*GP*GP*GP*GP*CP*CP*CP*GP*C)-3' / Coordinate model: P atoms only


Mass: 6381.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#4: RNA chain 5'-R(P*UP*GP*UP*UP*GP*GP*GP*UP*UP*AP*AP*GP*UP*CP*CP*CP*GP*CP*AP*AP*CP*GP*AP*G)-3' / Coordinate model: P atoms only


Mass: 7725.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

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30S ribosomal protein ... , 4 types, 4 molecules EFGH

#5: Protein 30S ribosomal protein S2 / / Coordinate model: Cα atoms only


Mass: 26671.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371
#6: Protein 30S ribosomal protein S7 / / Coordinate model: Cα atoms only


Mass: 17822.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#7: Protein 30S ribosomal protein S11 / / Coordinate model: Cα atoms only


Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376
#8: Protein 30S ribosomal protein S18 / / Coordinate model: Cα atoms only


Mass: 8483.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS

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Protein , 1 types, 1 molecules X

#9: Protein GTP-binding protein era / Coordinate model: Cα atoms only


Mass: 32863.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Details

Sequence detailsThe EM map on chain X, protein ERA, was obtained from Thermus thermophilus, but the coordinates ...The EM map on chain X, protein ERA, was obtained from Thermus thermophilus, but the coordinates were modeled based on Escherichia coli sequence.

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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
VitrificationCryogen 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: 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

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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 nucleic acid are present in the structure. The number of missing atoms was ...Details: projection matching using spider package. The coordinates for only the alpha carbons in protein and phosphoruses in nucleic acid 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 proteins and segments of RNA helices of the 30S subunit that contact era in the era-30S complex are included here.
Details: METHOD--Cross-correlation coefficient 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
21EGA

1ega

11EGA2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms869 86 0 0 955

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