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Open data
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Basic information
Entry | Database: PDB / ID: 5a9x | ||||||
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Title | Structure of GDP bound BipA | ||||||
![]() | GTP-BINDING PROTEIN | ||||||
![]() | RIBOSOMAL PROTEIN / BIPA / RIBOSOME / TRANSLATIONAL GTPASE FACTORS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kumar, V. / Chen, Y. / Ero, R. / Li, Z. / Gao, Y.-G. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.4 KB | Display | ![]() |
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PDB format | ![]() | 93.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6396C ![]() 6397C ![]() 5a9vC ![]() 5a9wC ![]() 5a9yC ![]() 5a9zC ![]() 5aa0C C: citing same article ( |
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Similar structure data |
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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 Details: TRANSLATIONAL GTPASE / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % / Description: NONE |
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Crystal grow | Details: 20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→47.45 Å / Num. obs: 10596 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 17.8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 14.96 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.8→47.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 89.909 / SU ML: 1.033 / Cross valid method: THROUGHOUT / ESU R Free: 0.783 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 240.067 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→47.45 Å
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