2LKD

IF2-G2 GDP complex

• PDB DOI: https://doi.org/10.2210/pdb2LKD/pdb
• BMRB: 6995

• Classification: TRANSLATION
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-10 Released: 2012-02-15 
• Deposition Author(s): Wienk, H., Tishchenko, E., Belardinelli, R., Tomaselli, S., Dongre, R., Spurio, R., Folkers, G.E., Gualerzi, C.O., Boelens, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 18 
• Selection Criteria: target function 

Literature

Structural Dynamics of Bacterial Translation Initiation Factor IF2.

Wienk, H., Tishchenko, E., Belardinelli, R., Tomaselli, S., Dongre, R., Spurio, R., Folkers, G.E., Gualerzi, C.O., Boelens, R.

(2012) J Biol Chem 287: 10922-10932

• PubMed: 22308033 
• DOI: https://doi.org/10.1074/jbc.M111.333393
• Primary Citation of Related Structures:  
  2LKC, 2LKD


• PubMed Abstract: 
  

  Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.

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Organizational Affiliation: 

Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.97 kDa 
• Atom Count: 1,392 
• Modelled Residue Count: 178 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-2	A	178	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: infB
UniProt
Find proteins for P04766 (Geobacillus stearothermophilus) Explore P04766  Go to UniProtKB:  P04766

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: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 18 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Wienk, H., Tishchenko, E., Belardinelli, R., Tomaselli, S., Dongre, R., Spurio, R., Folkers, G.E., Gualerzi, C.O., Boelens, R.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references