9BNI

X-ray crystal structure of Cu-TZ4H-H3AH10D tryptophan zipper metallo-beta-sheet peptide

• PDB DOI: https://doi.org/10.2210/pdb9BNI/pdb

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


• Deposited: 2024-05-02 Released: 2024-09-04 
• Deposition Author(s): Dang, V.T., Nguyen, A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 

Starting Model: experimental

Literature

Crystallography reveals metal-triggered restructuring of beta-hairpins.

Dang, V.T., Engineer, A., McElheny, D., Drena, A., Telser, J., Tomczak, K., Nguyen, A.I.

(2024) Chemistry : e202402101-e202402101

• PubMed: 39152095 
• DOI: https://doi.org/10.1002/chem.202402101
• Primary Citation of Related Structures:  
  9BNH, 9BNI


• PubMed Abstract: 
  

  Metal binding to β-sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo-β-sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β-sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ-helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12-residue β-sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X-ray diffraction (SC-XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher-order structures available to metallo-β-sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo-β-sheet peptides.

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Organizational Affiliation: 

University of Illinois Chicago, Chemistry, UNITED STATES.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 2.28 kDa 
• Atom Count: 183 
• Modelled Residue Count: 13 
• Deposited Residue Count: 13 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cu-TZ4H-H3AH10D tryptophan zipper metallo-beta-sheet peptide	A	13	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.518	α = 90
b = 45.518	β = 90
c = 45.518	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Dang, V.T., Nguyen, A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 2.0: 2024-09-25
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary