9CEQ | pdb_00009ceq

Lanthanide Binding Tag complex LBT3-NH2:La3+

• PDB DOI: https://doi.org/10.2210/pdb9CEQ/pdb
• BMRB: 31181

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2024-06-27 Released: 2024-07-17 
• Deposition Author(s): Kt, S., Messinger, R.J., Favaro, D.C.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

The Role of Asparagine as a Gatekeeper Residue in the Selective Binding of Rare Earth Elements by Lanthanide-Binding Peptides.

Kt, S.S., Qiao, B., Marmorstein, J.G., Wang, Y., Favaro, D.C., Stebe, K.J., Petersson, E.J., Radhakrishnan, R., de la Fuente-Nunez, C., Tu, R.S., Maldarelli, C., Olvera de la Cruz, M., Messinger, R.J.

(2025) Chemistry : e202501318-e202501318

• PubMed: 40312258 
• DOI: https://doi.org/10.1002/chem.202501318
• Primary Citation of Related Structures:  
  9CEQ


• PubMed Abstract: 
  

  Lanthanide-binding tag (LBT) peptides selectively complex lanthanide cations (Ln ³⁺ ) in their binding pockets and are promising for lanthanide separation. However, designing LBTs that selectively target specific Ln ³⁺ cations remains a challenge due to limited molecular-level understanding and control of interactions within the lanthanide-binding pocket. In this study, we reveal that the N5 asparagine residue acts as a gatekeeper in the binding pocket, resulting in a 100-fold selectivity for smaller Lu ³⁺ over larger La ³⁺ cations. Nuclear magnetic resonance spectroscopy and molecular dynamics simulations show that the N5 residue weakly binds to the larger La ³⁺ cation, permitting H ₂ O molecules inside the pocket. For the smaller Lu ³⁺ cations, the N5 residue forms an inter-arm hydrogen bond with the E14 glutamic acid residue, locking the Lu ³⁺ cation in the pocket and preventing H ₂ O infiltration. Mutating the N5 asparagine to a D5 aspartic acid prevents such a hydrogen bond, eliminating the gatekeeping mechanism and precipitously reducing selectivity. The resulting binding affinity to Ln ³⁺ cations is non-monotonic but generally increases with cation size. These results suggest a molecular design paradigm: the reduced affinity for larger lanthanides is due to open pocket conformations, while the selectivity of smaller Ln ³⁺ cations over larger ones is due to the gatekeeping hydrogen bond.

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Organizational Affiliation: 
• Department of Chemical Engineering, The City College of New York, CUNY, 160 Convent Ave, New York, NY, 10031, USA.
Department of Natural Sciences, Baruch College, City University of New York, 55 Lexington Ave, New York, NY, 10010, USA.
Department of Chemistry, University of Pennsylvania, 231 S 34th St, Philadelphia, PA, 19104, USA.
Department of Chemical and Biomolecular Engineering, University of Pennsylvania, 311A, 220 S 33rd St Towne Building, Philadelphia, PA, 19104, USA.
Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, 210 S 33rd St, Philadelphia, PA, 19104, USA.
Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St Nicholas Terrace, New York, NY, 10031, USA.
Departments of Microbiology and Psychiatry, Robert Wood Johnson Pavilion, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Department of Material Science and Engineering, Northwestern University, Room 2036, Cook Hall, 2220 Campus Drive, Evanston, IL, 60208, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 2.06 kDa 
• Atom Count: 137 
• Modeled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lanthanide Binding Tag Peptide	A	18	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LA (Subject of Investigation/LOI)	B [auth A]	LANTHANUM (III) ION La CZMAIROVPAYCMU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Kt, S., Messinger, R.J., Favaro, D.C.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0022240

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary
• Version 1.2: 2025-06-04
  Changes: Database references