2YOI

Crystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (LECA) from the Precambrian Period


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Conservation of protein structure over four billion years.

Ingles-Prieto, A.Ibarra-Molero, B.Delgado-Delgado, A.Perez-Jimenez, R.Fernandez, J.M.Gaucher, E.A.Sanchez-Ruiz, J.M.Gavira, J.A.

(2013) Structure 21: 1690-1697

  • DOI: 10.1016/j.str.2013.06.020
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating u ...

    Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis.


    Organizational Affiliation

    Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada 18071, Spain.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LECA THIOREDOXIN
A, B
106synthetic constructMutation(s): 0 
EC: 1.8.1.9
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.366α = 90
b = 47.772β = 98.49
c = 73.836γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Atomic model
  • Version 1.2: 2013-09-25
    Changes: Database references
  • Version 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Database references, Experimental preparation
  • Version 2.1: 2019-03-06
    Changes: Data collection, Experimental preparation