[English] 日本語
![](img/lk-miru.gif)
- PDB-3r9w: Crystal structure of Era in complex with MgGDPNP and nucleotides ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3r9w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Era in complex with MgGDPNP and nucleotides 1506-1542 of 16S ribosomal RNA | ||||||
![]() |
| ||||||
![]() | HYDROLASE/RNA / GTPase / KH domain / ribosome / biogenesis / GTP / 16S ribosomal RNA / GTP hydrolysis / HYDROLASE-RNA complex | ||||||
Function / homology | ![]() ribosomal small subunit binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / GTPase activity / GTP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tu, C. / Ji, X. | ||||||
![]() | ![]() Title: The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA. Authors: Tu, C. / Zhou, X. / Tarasov, S.G. / Tropea, J.E. / Austin, B.P. / Waugh, D.S. / Court, D.L. / Ji, X. #1: ![]() Title: Structure of ERA in complex with the 3' end of 16S rRNA: Implications for ribosome biogenesis Authors: Tu, C. / Zhou, X. / Tropea, J.E. / Austin, B.P. / Waugh, D.S. / Court, L.D. / Ji, X. #2: ![]() 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3r9xC ![]() 3ievS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 34765.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: RNA chain | Mass: 10905.535 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Aquifex aeolicus except for U1506 that is replaced with C1506. |
-Non-polymers , 6 types, 101 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-GNP / | ||||||
#5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | ChemComp-CA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M calcium acetate, 40% (v/v) MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2008 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→30 Å / Num. obs: 27524 / % possible obs: 93.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.078 / Χ2: 0.981 / Net I/σ(I): 14.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3IEV Resolution: 2.05→25.913 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.738 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.07 Å2 / Biso mean: 62.1928 Å2 / Biso min: 30.16 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→25.913 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|