5CEG | pdb_00005ceg

X-ray structure of toxin/anti-toxin complex from Mesorhizobium opportunistum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5CEG

This is version 1.3 of the entry. See complete history

Literature

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates.

Aakre, C.D.Herrou, J.Phung, T.N.Perchuk, B.S.Crosson, S.Laub, M.T.

(2015) Cell 163: 594-606

  • DOI: https://doi.org/10.1016/j.cell.2015.09.055
  • Primary Citation Related Structures: 
    5CEG

  • PubMed Abstract: 

    Interacting proteins typically coevolve, and the identification of coevolving amino acids can pinpoint residues required for interaction specificity. This approach often assumes that an interface-disrupting mutation in one protein drives selection of a compensatory mutation in its partner during evolution. However, this model requires a non-functional intermediate state prior to the compensatory change. Alternatively, a mutation in one protein could first broaden its specificity, allowing changes in its partner, followed by a specificity-restricting mutation. Using bacterial toxin-antitoxin systems, we demonstrate the plausibility of this second, promiscuity-based model. By screening large libraries of interface mutants, we show that toxins and antitoxins with high specificity are frequently connected in sequence space to more promiscuous variants that can serve as intermediates during a reprogramming of interaction specificity. We propose that the abundance of promiscuous variants promotes the expansion and diversification of toxin-antitoxin systems and other paralogous protein families during evolution.


  • Organizational Affiliation
    • Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Macromolecule Content 

  • Total Structure Weight: 49.9 kDa 
  • Atom Count: 3,685 
  • Modeled Residue Count: 374 
  • Deposited Residue Count: 420 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Addiction module antidote protein, CopG/Arc/MetJ family
A, C
93Mesorhizobium opportunistum WSM2075Mutation(s): 0 
Gene Names: Mesop_5599
UniProt
Find proteins for F7YBW8 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Explore F7YBW8 
Go to UniProtKB:  F7YBW8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7YBW8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasmid stabilization system
B, D
117Mesorhizobium opportunistum WSM2075Mutation(s): 0 
Gene Names: Mesop_5598
UniProt
Find proteins for F7YBW7 (Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075))
Explore F7YBW7 
Go to UniProtKB:  F7YBW7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7YBW7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
K [auth B]
M [auth C]
Q [auth D]
F [auth A],
G [auth A],
K [auth B],
M [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
H [auth B]
I [auth B]
L [auth C]
N [auth D]
E [auth A],
H [auth B],
I [auth B],
L [auth C],
N [auth D],
O [auth D],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
J [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.18α = 90
b = 118.84β = 90
c = 211.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations