5A9X | pdb_00005a9x

Structure of GDP bound BipA

• PDB DOI: https://doi.org/10.2210/pdb5A9X/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-23 Released: 2015-08-26 
• Deposition Author(s): Kumar, V., Chen, Y., Ero, R., Li, Z., Gao, Y.-G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.313 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.268 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Literature

Structure of Bipa in GTP Form Bound to the Ratcheted Ribosome.

Kumar, V., Chen, Y., Ero, R., Ahmed, T., Tan, J., Li, Z., Wong, A.S.W., Bhushan, S., Gao, Y.

(2015) Proc Natl Acad Sci U S A 112: 10944

• PubMed: 26283392 
• DOI: https://doi.org/10.1073/pnas.1513216112
• Primary Citation Related Structures: 
  5A9V, 5A9W, 5A9X, 5A9Y, 5A9Z, 5AA0


• PubMed 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 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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Organizational Affiliation: 
• Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore;
School of Biological Sciences, Nanyang Technological University, 637551, Singapore [e-mail] [e-mail].
Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.88 kDa 
• Atom Count: 4,167 
• Modeled Residue Count: 556 
• Deposited Residue Count: 607 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-BINDING PROTEIN	A	607	Escherichia coli	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for P0A3B2 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore P0A3B2  Go to UniProtKB:  P0A3B2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.313 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.268 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 241.946	α = 90
b = 241.946	β = 90
c = 241.946	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Kumar, V., Chen, Y., Ero, R., Li, Z., Gao, Y.-G.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 1.2: 2015-09-16
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other