5DQY | pdb_00005dqy

A fully oxidized human thioredoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5DQY

This is version 1.1 of the entry. See complete history

Literature

Crystal structure of fully oxidized human thioredoxin.

Hwang, J.Nguyen, L.T.Jeon, Y.H.Lee, C.Y.Kim, M.H.

(2015) Biochem Biophys Res Commun 467: 218-222

  • DOI: https://doi.org/10.1016/j.bbrc.2015.10.003
  • Primary Citation Related Structures: 
    5DQY

  • PubMed Abstract: 

    In addition to the active cysteines located at positions 32 and 35 in humans, mammalian cytosolic thioredoxin (TRX) possesses additional conserved cysteine residues at positions 62, 69, and 73. These non-canonical cysteine residues, that are distinct from prokaryotic TRX and also not found in mammalian mitochondrial TRX, have been implicated in biological functions regulating signal transduction pathways via their post-translational modifications. Here, we describe for the first time the structure of a fully oxidized TRX. The structure shows a non-active Cys62-Cys69 disulfide bond in addition to the active Cys32-Cys35 disulfide. The non-active disulfide switches the α3-helix of TRX, composed of residues Cys62 to Glu70, to a bulging loop and dramatically changes the environment of the TRX residues involved in the interaction with its reductase and other cellular substrates. This structural modification may have implications for a number of potential functions of TRX including the regulation of redox-dependent signaling pathways.


  • Organizational Affiliation
    • Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea.

Macromolecule Content 

  • Total Structure Weight: 12 kDa 
  • Atom Count: 964 
  • Modeled Residue Count: 105 
  • Deposited Residue Count: 105 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin105Homo sapiensMutation(s): 0 
Gene Names: TXNTRDXTRXTRX1
UniProt & NIH Common Fund Data Resources
Find proteins for P10599 (Homo sapiens)
Explore P10599 
Go to UniProtKB:  P10599
PHAROS:  P10599
GTEx:  ENSG00000136810 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10599
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.204α = 90
b = 61.231β = 90
c = 64.839γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2015-12-23 
  • Deposition Author(s): Hwang, J.

Funding OrganizationLocationGrant Number
KRIBBKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary