Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.12 kDa 
• Atom Count: 744 
• Modelled Residue Count: 84 
• Deposited Residue Count: 84 
• Unique protein chains: 1

5UGK

Zinc-Binding Structure of a Catalytic Amyloid from Solid-State NMR Spectroscopy

• PDB DOI: 10.2210/pdb5UGK/pdb
• BMRB: 30227

• Classification: METAL BINDING PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-01-09 Released: 2017-05-31 
• Deposition Author(s): Lee, M., Wang, T., Makhlynets, O.V., Wu, Y., Polizzi, N., Wu, H., Gosavi, P.M., Korendovych, I.V., DeGrado, W.F., Hong, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Zinc-binding structure of a catalytic amyloid from solid-state NMR.

Lee, M., Wang, T., Makhlynets, O.V., Wu, Y., Polizzi, N.F., Wu, H., Gosavi, P.M., Stohr, J., Korendovych, I.V., DeGrado, W.F., Hong, M.

(2017) Proc Natl Acad Sci U S A 114: 6191-6196

• PubMed: 28566494 
• DOI: 10.1073/pnas.1706179114
• Primary Citation of Related Structures:  
  5UGK


• PubMed Abstract: 
  

Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive backbones for advanced materials. When β-strands of an amyloid are arranged parallel and in register, side chains from the same position of each chain align, facilitating metal chelation when the residues are good ligands such as histidine. High-resolution structures of metalloamyloids are needed to understand the molecular bases of metal-amyloid interactions. Here we combine solid-state NMR and structural bioinformatics to determine the structure of a zinc-bound metalloamyloid that catalyzes ester hydrolysis. The peptide forms amphiphilic parallel β-sheets that assemble into stacked bilayers with alternating hydrophobic and polar interfaces. The hydrophobic interface is stabilized by apolar side chains from adjacent sheets, whereas the hydrated polar interface houses the Zn ²⁺ -binding histidines with binding geometries unusual in proteins. Each Zn ²⁺ has two bis-coordinated histidine ligands, which bridge adjacent strands to form an infinite metal-ligand chain along the fibril axis. A third histidine completes the protein ligand environment, leaving a free site on the Zn ²⁺ for water activation. This structure defines a class of materials, which we call metal-peptide frameworks. The structure reveals a delicate interplay through which metal ions stabilize the amyloid structure, which in turn shapes the ligand geometry and catalytic reactivity of Zn ² .

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Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-HIS-VAL-HIS-LEU-GLN-ILE	A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K], G [auth O], H [auth Q], I [auth S], J [auth U], K [auth W], L [auth Y]	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth A], N [auth C], O [auth E], P [auth G], Q [auth I], R [auth K], S [auth O], T [auth Q], U [auth S], V [auth U], W, X [auth Y]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 5UGK Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-09 
• Released Date: 2017-05-31 
Deposition Author(s): Lee, M., Wang, T., Makhlynets, O.V., Wu, Y., Polizzi, N., Wu, H., Gosavi, P.M., Korendovych, I.V., DeGrado, W.F., Hong, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM066976
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119634
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	P01AG002132

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Database references
• Version 1.2: 2017-06-28
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2019-12-18
  Changes: Author supporting evidence, Data collection