9GGO | pdb_00009ggo

Strand-swapped dimer of engineered copper binding SH3-like protein

• PDB DOI: https://doi.org/10.2210/pdb9GGO/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-13 Released: 2025-01-15 
• Deposition Author(s): Schwan, M., Kopp, J., Sinning, I.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: in silico

Literature

Strand-Swapped SH3 Domain Dimer with Superoxide Dismutase Activity.

Hage, F.R., Schwan, M., Conde Gonzalez, M.R., Huber, J., Germer, S., Macri, M., Kopp, J., Sinning, I., Thomas, F.

(2025) ACS Cent Sci 11: 157-166

• PubMed: 39866698 
• DOI: https://doi.org/10.1021/acscentsci.4c01347
• Primary Citation Related Structures: 
  9GGO


• PubMed Abstract: 
  

  The design of metalloproteins allows us to better understand metal complexation in proteins and the resulting function. In this study, we incorporated a Cu ²⁺ -binding site into a natural protein domain, the 58 amino acid c-Crk-SH3, to create a miniaturized superoxide dismutase model, termed SO1. The resulting low complexity metalloprotein was characterized for structure and function by circular dichroism and UV spectroscopy as well as EPR spectroscopy and X-ray crystallography. The miniprotein was found to be a strand-swapped dimer with an unusual coupled binuclear Type 2-like copper center in each protomer. SO1-Cu was found to be SOD-active with an activity only 1 order of magnitude lower than that of natural SOD enzymes and 1 to 2 orders of magnitude higher than that of other low-complexity SOD protein models of similar size. This serendipitous design provides us with a new structural template for future designs of binuclear metalloproteins with different metal ions and functions.

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Organizational Affiliation: 
• Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany.
Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
Max Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 7.06 kDa 
• Atom Count: 511 
• Modeled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SH3-like protein	A	58	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU (Subject of Investigation/LOI)	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.509	α = 90
b = 56.509	β = 90
c = 58.778	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Schwan, M., Kopp, J., Sinning, I.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SI 586-6

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-02-05
  Changes: Database references