5C2N

The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints.

Smock, R.G.Yadid, I.Dym, O.Clarke, J.Tawfik, D.S.

(2016) Cell 164: 476-486

  • DOI: 10.1016/j.cell.2015.12.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-p ...

    Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-propeller proteins, a globular and symmetric fold group with diverse functions. The identification of short propeller-like motifs (<50 amino acids) in natural genomes indicated that they expanded via tandem duplications to form extant propellers. We phylogenetically reconstructed 47-residue ancestral motifs that form five-bladed lectin propellers via oligomeric assembly. We demonstrate a functional trajectory of tandem duplications of these motifs leading to monomeric lectins. Foldability, i.e., higher efficiency of folding, was the main parameter leading to improved functionality along the entire evolutionary trajectory. However, folding constraints changed along the trajectory: initially, conflicts between monomer folding and oligomer assembly dominated, whereas subsequently, upon tandem duplication, tradeoffs between monomer stability and foldability took precedence.


    Organizational Affiliation

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta propeller
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
48Enterobacteria phage L1Mutation(s): 0 
Find proteins for A0A140UHM9 (Enterobacteria phage L1)
Go to UniProtKB:  A0A140UHM9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, I, J, L, M, O
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.186 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 112.219α = 90.00
b = 112.219β = 90.00
c = 107.290γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2016-02-10
    Type: Database references