9G8I | pdb_00009g8i

Sumo-Darpin-A10-complex

• PDB DOI: https://doi.org/10.2210/pdb9G8I/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): synthetic construct, Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-23 Released: 2025-03-05 
• Deposition Author(s): Cakilkaya, B., Wolf, E., Boergel, A.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.301 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast.

Troster, V., Wong, R.P., Borgel, A., Cakilkaya, B., Renz, C., Mockel, M.M., Eifler-Olivi, K., Marinho, J., Reinberg, T., Furler, S., Schaefer, J.V., Pluckthun, A., Wolf, E., Ulrich, H.D.

(2025) Cell Rep 44: 115353-115353

• PubMed: 40019834 
• DOI: https://doi.org/10.1016/j.celrep.2025.115353
• Primary Citation Related Structures: 
  9G8I, 9GAU


• PubMed Abstract: 
  

  The small ubiquitin-related modifier SUMO regulates cellular processes in eukaryotes either by modulating individual protein-protein interactions or with relaxed substrate selectivity by group modification. Here, we report the isolation and characterization of designed ankyrin repeat protein (DARPin)-based affinity probes directed against budding yeast SUMO (Smt3). We validate selected DARPins as compartment-specific inhibitors or neutral detection agents. Structural characterization reveals a recognition mode distinct from that of natural SUMO interactors. In vivo application pinpoints Smt3's essential function to the nucleus and demonstrates DARPin-mediated sensitization toward various stress conditions. A subset of selected clones is validated as SUMOylation reporters in cells. In this manner, we identify a DNA-damage-induced nuclear SUMOylation response that-in contrast to previously reported chromatin group SUMOylation-is independent of single-stranded DNA and the SUMO-E3 Siz2 but depends on Mms21 and likely reflects late intermediates of homologous recombination. Thus, Smt3-specific DARPins can provide insight into the dynamics of SUMOylation in defined subcellular structures.

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Organizational Affiliation: 
• Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
Institute of Molecular Physiology, Johannes Gutenberg University, 55128 Mainz, Germany.
Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.29 kDa 
• Atom Count: 3,506 
• Modeled Residue Count: 461 
• Deposited Residue Count: 464 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin	A, C [auth B]	157	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3	B [auth C], D	75	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SMT3, YDR510W, D9719.15
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.301 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.972	α = 90
b = 94.747	β = 90
c = 120.957	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Cakilkaya, B., Wolf, E., Boergel, A.

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

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-03-12
  Changes: Database references
• Version 2.0: 2025-06-11
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary