9ML0 | pdb_00009ml0

Co-MAHF-9 A8Q Hydrated Metal Alpha-Helix Framework

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2024-12-18 Released: 2025-05-21 
  • Deposition Author(s): Richardson-Matthews, R.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Metal-alpha-Helix Peptide Frameworks.

Richardson-Matthews, R.Velko, K.Bhunia, B.Ghosh, S.Oktawiec, J.Brunzelle, J.S.Dang, V.T.Nguyen, A.I.

(2025) J Am Chem Soc 147: 17433-17447

  • DOI: https://doi.org/10.1021/jacs.5c04078
  • Primary Citation of Related Structures:  
    9EFY, 9EG0, 9EG2, 9EG3, 9EG5, 9EH3, 9EHN, 9EHP, 9EHQ, 9EJU, 9EJV, 9MDB, 9MDG, 9MEO, 9MEP, 9MEQ, 9MFI, 9MFJ, 9MFK, 9MKJ, 9ML0, 9MNV

  • PubMed Abstract: 

    Metal-peptide frameworks (MPFs) are a growing class of metal-organic frameworks with promising applications in metalloprotein mimicry, chiral separations, and catalysis. There are limited examples of MPFs, especially those with both secondary structure and natural amino acid side chains that coordinate to metal nodes, which are important for accurately mimicking metalloprotein active sites. Here, we design a robust and modular strategy based on short α-helical peptides (nine amino acids long) to form frameworks with many types of biomimetic metal sites. Peptides were designed to have Glu and His metal-binding residues, hydrophobic residues, and noncanonical helix-enforcing residues. With Co(II), it was shown that mutagenesis of a single amino acid near the metal-binding residues generates a diverse library of frameworks with varying metal node coordination geometries and compositions. Structures for 16 out of 20 variants were characterized by single-crystal X-ray diffraction, revealing how noncovalent interactions impact the metal primary sphere. In one case, a point mutation turns on reversible ligand-triggered conformational changes, demonstrating that this platform allows for dynamic behavior like that observed in metalloproteins. Furthermore, we show that frameworks readily assemble with Mn(II), Fe(II), Cu(II), and Zn(II) ions, highlighting the generality of this approach. The ease-of-synthesis, modularity, and crystallinity of these materials make this a highly accessible platform for studying and engineering biomimetic metal centers in porous materials.


  • Organizational Affiliation
    • Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States.

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Co-MAHF-9 A8Q Hydrated
A, B, C, D
11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
A, B, C, D
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 16.206α = 90
b = 46.634β = 106.2
c = 19.845γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM15479301
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Database references