Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.53 kDa 
• Atom Count: 449 
• Modelled Residue Count: 56 
• Deposited Residue Count: 56 
• Unique protein chains: 1

2AYJ

Solution structure of 50S ribosomal protein L40e from Sulfolobus solfataricus

• PDB DOI: 10.2210/pdb2AYJ/pdb

• Classification: TRANSLATION
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-07 Released: 2006-08-22 
• Deposition Author(s): Wu, B., Yee, A., Lukin, J., Lemak, A., Semesi, A., Ramelot, T., Kennedy, M., Edward, A., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of ribosomal protein L40E, a unique C4 zinc finger protein encoded by archaeon Sulfolobus solfataricus

Wu, B., Lukin, J., Yee, A., Lemak, A., Semesi, A., Ramelot, T.A., Kennedy, M.A., Arrowsmith, C.H.

(2008) Protein Sci 17: 589-596

• PubMed: 18218710 
• DOI: 10.1110/ps.073273008
• Primary Citation of Related Structures:  
  2AYJ


• PubMed Abstract: 
  

The ribosomal protein L40E from archaeon Sulfolobus solfataricus is a component of the 50S ribosomal subunit. L40E is a 56-residue, highly basic protein that contains a C4 zinc finger motif, CRKC_X(10)_CRRC. Homologs are found in both archaea and eukaryotes but are not present in bacteria. Eukaryotic genomes encode L40E as a ubiquitin-fusion protein. L40E was absent from the crystal structure of euryarchaeota 50S ribosomal subunit. Here we report the three-dimensional solution structure of L40E by NMR spectroscopy. The structure of L40E is a three-stranded beta-sheet with a simple beta2beta1beta3 topology. There are two unique characteristics revealed by the structure. First, a large and ordered beta2-beta3 loop twists to pack across the one side of the protein. L40E contains a buried polar cluster comprising Lys19, Lys20, Cys22, Asn29, and Cys36. Second, the surface of L40E is almost entirely positively charged. Ten conserved basic residues are positioned on the two sides of the surface. It is likely that binding of zinc is essential in stabilizing the tertiary structure of L40E to act as a scaffold to create a broad positively charged surface for RNA and/or protein recognition.

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Organizational Affiliation: 

Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L40e	A	56	Saccharolobus solfataricus	Mutation(s): 0  Gene Names: rpl40e
UniProt
Find proteins for Q980V5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q980V5  Go to UniProtKB:  Q980V5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2AYJ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-07 
• Released Date: 2006-08-22 
Deposition Author(s): Wu, B., Yee, A., Lukin, J., Lemak, A., Semesi, A., Ramelot, T., Kennedy, M., Edward, A., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-08-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations