2JZ7 | pdb_00002jz7

Solution NMR structure of selenium-binding protein from Methanococcus Vannielii


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 2JZ7

This is version 1.3 of the entry. See complete history

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 Biological Chem 283: 25936-25943

  • DOI: https://doi.org/10.1074/jbc.M803773200
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 44.06 kDa 
  • Atom Count: 3,085 
  • Modeled Residue Count: 405 
  • Deposited Residue Count: 405 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Selenium binding protein
A, B, C, D, E
81Methanococcus vannieliiMutation(s): 0 
Gene Names: sbp
UniProt
Find proteins for Q5UBU1 (Methanococcus vannielii)
Explore Q5UBU1 
Go to UniProtKB:  Q5UBU1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UBU1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-05-29
    Changes: Data collection