9BNH

X-ray Crystal Structure of Cu-TZ4H tryptophan Zipper Metallo-Peptide

PDB DOI: https://doi.org/10.2210/pdb9BNH/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.145
R-Value Work: 0.119
R-Value Observed: 0.122

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

University of Illinois Chicago, Chemistry, UNITED STATES.

Macromolecule Content

Total Structure Weight: 4.18 kDa
Atom Count: 348
Modelled Residue Count: 24
Deposited Residue Count: 24
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cu-TZ4H tryptophan Zipper Metallo-Peptide	A, B	12	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain P [auth B]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B]	E [auth A], O [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A] I [auth B] J [auth B] K [auth B] L [auth B] D [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A]
NH3 Query on NH3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	AMMONIA H₃ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B]