[English] 日本語
Yorodumi- EMDB-6397: The structure of BipA in GTP form bound to the ratcheted ribosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6397 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of BipA in GTP form bound to the ratcheted ribosome | |||||||||
Map data | Reconstruction of BipA bound to 70S in complex with tRNAs and mRNA | |||||||||
Sample |
| |||||||||
Keywords | Ribosome / BipA | |||||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / protein folding chaperone / response to cold / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly ...guanosine tetraphosphate binding / protein folding chaperone / response to cold / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / response to heat / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Kumar V / Chen Y / Ero R / Ahmed T / Tan J / Li Z / Wong ASW / Gao Y-G / Bhushan S | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structure of BipA in GTP form bound to the ratcheted ribosome. Authors: Veerendra Kumar / Yun Chen / Rya Ero / Tofayel Ahmed / Jackie Tan / Zhe Li / Andrew See Weng Wong / Shashi Bhushan / Yong-Gui Gao / Abstract: BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly ...BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6397.map.gz | 31.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6397-v30.xml emd-6397.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | 400_6397.gif 80_6397.gif | 92.6 KB 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6397 | HTTPS FTP |
-Validation report
Summary document | emd_6397_validation.pdf.gz | 293 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6397_full_validation.pdf.gz | 292.1 KB | Display | |
Data in XML | emd_6397_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6397 | HTTPS FTP |
-Related structure data
Related structure data | 5aa0MC 6396C 5a9vC 5a9wC 5a9xC 5a9yC 5a9zC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6397.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of BipA bound to 70S in complex with tRNAs and mRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : BipA bound to 70S in complex with tRNAs and mRNA
Entire | Name: BipA bound to 70S in complex with tRNAs and mRNA |
---|---|
Components |
|
-Supramolecule #1000: BipA bound to 70S in complex with tRNAs and mRNA
Supramolecule | Name: BipA bound to 70S in complex with tRNAs and mRNA / type: sample / ID: 1000 / Number unique components: 2 |
---|---|
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa / Method: Sedimentation |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S, SSU 30S, PSR16s, ALL |
---|---|
Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Macromolecule #1: BipA
Macromolecule | Name: BipA / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 5 mM HEPES, pH 7.5, 10 mM MgOAc, 50 mM KCl, 10 mM NH4Cl, 6 mM 2-mercaptoethanol |
---|---|
Grid | Details: 300 mesh copper grid with 2 nm carbon support, glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 73684 times magnification. |
Date | May 7, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1531 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 109375 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected using EMAN and processed using Relion. |
---|---|
CTF correction | Details: CTFfind |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 77127 |