Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 35990.19 
• Atom Count: 2406 
• Residue Count: 326 
• Unique protein chains: 1

4TOI

Crystal structure of E.coli ribosomal protein S2 in complex with N-terminal domain of S1

• DOI: 10.2210/pdb4TOI/pdb

• Classification: RIBOSOMAL PROTEIN
• Expression System: Escherichia coli


• Deposited: 2014-06-05 Released: 2014-12-31 
• Deposition Author(s): Grishkovskaya, I., Byrgazov, K., Moll, I., Djinovic-Carugo, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.229 
• R-Value Work: 0.164 

Literature

Structural basis for the interaction of protein S1 with the Escherichia coli ribosome.

Byrgazov, K., Grishkovskaya, I., Arenz, S., Coudevylle, N., Temmel, H., Wilson, D.N., Djinovic-Carugo, K., Moll, I.

(2015) Nucleic Acids Res. 43: 661-673

• PubMed: 25510494 
• DOI: 10.1093/nar/gku1314


• PubMed Abstract: 
  

In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to its functional importance, S1 is still lacking from the high-resolution structures available for Escherichia coli and Thermus thermophilus ribosomes and thus the molecular mechanism governing the S1-ribosome interaction has still remained elusive. Here, we present the structure of the N-terminal S1 domain D1 when bound to the ribosome at atomic resolution by using a combination of NMR, X-ray crystallography and cryo-electron microscopy. Together with biochemical assays, the structure reveals that S1 is anchored to the ribosome primarily via a stabilizing π-stacking interaction within the short but conserved N-terminal segment that is flexibly connected to domain D1. This interaction is further stabilized by salt bridges involving the zinc binding pocket of protein S2. Overall, this work provides one hitherto enigmatic piece in the 'ribosome puzzle', namely the detailed molecular insight into the topology of the S1-ribosome interface. Moreover, our data suggest novel mechanisms that have the potential to modulate protein synthesis in response to environmental cues by changing the affinity of S1 for the ribosome.

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Organizational Affiliation: 

Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Centre for Molecular Biology, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2,Ribosomal protein S1	A	326	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.229 
• R-Value Work: 0.164 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 87.280	α = 90.00
b = 87.280	β = 90.00
c = 94.360	γ = 120.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PDB_EXTRACT	data extraction
XSCALE	data reduction
BALBES	phasing
XDS	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-05 
• Released Date: 2014-12-31 
• Deposition Author(s): Grishkovskaya, I., Byrgazov, K., Moll, I., Djinovic-Carugo, K.

Revision History 

• Version 1.0: 2014-12-31
  Type: Initial release
• Version 1.1: 2015-01-21
  Type: Database references