+Open data
-Basic information
Entry | Database: PDB / ID: 5a9w | ||||||
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Title | Structure of GDPCP BipA | ||||||
Components | GTP-BINDING PROTEIN | ||||||
Keywords | RIBOSOMAL PROTEIN / RIBOSOME / TRANSLATIONAL GTPASE FACTORS | ||||||
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 / ribosome biogenesis / ribosome binding / response to heat / tRNA binding / rRNA binding / ribonucleoprotein complex ...guanosine tetraphosphate binding / protein folding chaperone / response to cold / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome biogenesis / ribosome binding / response to heat / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Kumar, V. / Chen, Y. / Ero, R. / Li, Z. / Gao, Y. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a9w.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a9w.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 5a9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a9w_validation.pdf.gz | 675.5 KB | Display | wwPDB validaton report |
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Full document | 5a9w_full_validation.pdf.gz | 706.2 KB | Display | |
Data in XML | 5a9w_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 5a9w_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a9w ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a9w | HTTPS FTP |
-Related structure data
Related structure data | 6396C 6397C 5a9vC 5a9xC 5a9yC 5a9zC 5aa0C 3e3xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 67439.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA T1R / References: UniProt: B7MHF0, UniProt: P0DTT0*PLUS |
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#2: Chemical | ChemComp-GCP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.66→48.49 Å / Num. obs: 12870 / % possible obs: 99.5 % / Observed criterion σ(I): 2.1 / Redundancy: 18.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.66→3.86 Å / Redundancy: 17.3 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E3X Resolution: 3.7→48.49 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 47.304 / SU ML: 0.66 / Cross valid method: THROUGHOUT / ESU R Free: 0.718 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 152.456 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→48.49 Å
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