9BNI | pdb_00009bni

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BNI

This is version 2.1 of the entry. See complete history

Literature

Crystallography Reveals Metal-Triggered Restructuring of beta-Hairpins.

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

(2024) Chemistry 30: e202402101-e202402101

  • DOI: https://doi.org/10.1002/chem.202402101
  • Primary Citation 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.


  • Organizational Affiliation
    • University of Illinois Chicago, Chemistry, UNITED STATES.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cu-TZ4H-H3AH10D tryptophan zipper metallo-beta-sheet peptide13synthetic constructMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
D [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
C [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
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 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.518α = 90
b = 45.518β = 90
c = 45.518γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-11-06
    Changes: Database references, Structure summary