9D5A | pdb_00009d5a

Structure of Citrobacter multi-ubiquitin protein, local refinement of one full-length protomer

• PDB DOI: https://doi.org/10.2210/pdb9D5A/pdb
• EM Map EMD-46577: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Citrobacter sp. RHBSTW-00271
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-13 Released: 2025-04-02 
• Deposition Author(s): Gong, M., Gu, Y., Corbett, K.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural diversity and oligomerization of bacterial ubiquitin-like proteins.

Gong, M., Ye, Q., Gu, Y., Chambers, L.R., Bobkov, A.A., Arakawa, N.K., Matyszewski, M., Corbett, K.D.

(2025) Structure 33: 1016-1026.e4

• PubMed: 40250427 
• DOI: https://doi.org/10.1016/j.str.2025.03.011
• Primary Citation Related Structures: 
  8U38, 9CD2, 9D59, 9D5A, 9D5B


• PubMed Abstract: 
  

  Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca ²⁺ ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca ²⁺ -mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.

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Organizational Affiliation: 
• Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Environmental and Complex Analysis Laboratory, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
UC San Diego Cryo-EM Facility, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 28.58 kDa 
• Atom Count: 1,704 
• Modeled Residue Count: 212 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multi-ubiquitin domain-containing protein	A	247	Citrobacter sp. RHBSTW-00271	Mutation(s): 0
UniProt
Find proteins for A0A5B0SRH6 (Citrobacter portucalensis) Explore A0A5B0SRH6  Go to UniProtKB:  A0A5B0SRH6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Gong, M., Gu, Y., Corbett, K.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM144121

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-04-30
  Changes: Data collection, Database references
• Version 1.2: 2025-06-18
  Changes: Data collection, Database references