8DQ2

X-ray crystal structure of Hansschlegelia quercus lanmodulin (LanM) with lanthanum (III) bound at pH 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer.

Mattocks, J.A.Jung, J.J.Lin, C.Y.Dong, Z.Yennawar, N.H.Featherston, E.R.Kang-Yun, C.S.Hamilton, T.A.Park, D.M.Boal, A.K.Cotruvo Jr., J.A.

(2023) Nature 618: 87-93

  • DOI: https://doi.org/10.1038/s41586-023-05945-5
  • Primary Citation of Related Structures:  
    8DQ2, 8FNR, 8FNS

  • PubMed Abstract: 

    Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number 1-3 . The natural lanthanide-binding protein lanmodulin (LanM) 4,5 is a sustainable alternative to conventional solvent-extraction-based separation 6 . Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM's quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM's greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.


  • Organizational Affiliation

    Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing protein
A, B, C, D
110Hansschlegelia quercusMutation(s): 0 
Gene Names: EYR15_14300
UniProt
Find proteins for A0A4V2JDD3 (Hansschlegelia quercus)
Explore A0A4V2JDD3 
Go to UniProtKB:  A0A4V2JDD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V2JDD3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
I [auth B],
R [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
LA (Subject of Investigation/LOI)
Query on LA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
U [auth D]
LANTHANUM (III) ION
La
CZMAIROVPAYCMU-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
Q [auth C],
V [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.107α = 90
b = 108.658β = 90.02
c = 44.697γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection