Biological Assembly 1  

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

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.06 kDa 
• Atom Count: 3085 
• Modelled Residue Count: 405 
• Deposited Residue Count: 405 
• Unique protein chains: 1

2JZ7

Solution NMR structure of selenium-binding protein from Methanococcus Vannielii

• PDB DOI: 10.2210/pdb2JZ7/pdb

• Classification: Selenium-Binding Protein
• Organism(s): Methanococcus vannielii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-28 Released: 2008-07-22 
• Deposition Author(s): Suzuki, M., Stadtman, T.C., Tjandra, N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution NMR Structure of Selenium-binding Protein from Methanococcus vannielii.

Suzuki, M., Lee, D.Y., Inyamah, N., Stadtman, T.C., Tjandra, N.

(2008) J Biol Chem 283: 25936-25943

• PubMed: 18650445 
• DOI: 10.1074/jbc.M803773200
• Primary Citation of Related Structures:  
  2JZ7


• PubMed Abstract: 
  

Selenium is an important nutrient. The lack of selenium will suppress expression of various enzymes that will lead to cell abnormality and diseases. However, high concentrations of free selenium are toxic to the cell because it adversely affects numerous cell metabolic pathways. In Methanococcus vannielii, selenium transport in the cell is established by the selenium-binding protein, SeBP. SeBP sequesters selenium during transport, thus regulating the level of free selenium in the cell, and delivers it specifically to the selenophosphate synthase enzyme. In solution, SeBP is an oligomer of 8.8-kDa subunits. It is a symmetric pentamer. The solution structure of SeBP was determined by NMR spectroscopy. Each subunit of SeBP is composed of an alpha-helix on top of a 4-stranded twisted beta-sheet. The stability of the five subunits stems mainly from hydrophobic interactions and supplemented by hydrogen bond interactions. The loop containing Cys(59) has been shown to be important for selenium binding, is flexible, and adopts multiple conformations. However, the cysteine accessibility is restricted in the structure, reducing the possibility of the binding of free selenium readily. Therefore, a different selenium precursor or other factors might be needed to facilitate opening of this loop to expose Cys(59) for selenium binding.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Selenium binding protein	A, B, C, D, E	81	Methanococcus vannielii	Mutation(s): 0  Gene Names: sbp
UniProt
Find proteins for Q5UBU1 (Methanococcus vannielii) Explore Q5UBU1  Go to UniProtKB:  Q5UBU1

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2JZ7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-28 
• Released Date: 2008-07-22 
Deposition Author(s): Suzuki, M., Stadtman, T.C., Tjandra, N.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations