9DSM | pdb_00009dsm

Cryo-EM structure of SSNA-1(R18E/R20E/Q98E) filaments

• PDB DOI: https://doi.org/10.2210/pdb9DSM/pdb
• EM Map EMD-47147: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-09-27 Released: 2025-08-27 
• Deposition Author(s): Agostini, L., Biertumpfel, C., Mizuno, N.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.55 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: in silico

Literature

Structural insights into SSNA1 self-assembly and its microtubule binding for centriole maintenance.

Agostini, L., Pfister, J.A., Basnet, N., Ding, J., Zhang, R., Biertumpfel, C., O'Connell, K.F., Mizuno, N.

(2025) Nat Commun 16: 7512-7512

• PubMed: 40804232 
• DOI: https://doi.org/10.1038/s41467-025-62696-9
• Primary Citation Related Structures: 
  9DSM


• PubMed Abstract: 
  

  SSNA1 is a fibrillar protein involved in dynamic microtubule remodeling, including nucleation, co-polymerization, and microtubule branching. The underlying molecular mechanism has remained unclear due to a lack of structural information. Here, we determine the cryo-EM structure of C.elegans SSNA-1 at 4.55-Å resolution and evaluate its role in embryonic development. We find that SSNA-1 forms an anti-parallel coiled-coil, with self-assembly facilitated by an overhang of 16 C-terminal residues that form a triple-stranded helical junction. The microtubule-binding region is within the triple-stranded junction, suggesting that self-assembly of SSNA-1 creates hubs for effective microtubule interaction. Genetical analysis elucidates that SSNA-1 deletion significantly reduces embryonic viability, and causes multipolar spindles during cell division. Interestingly, impairing SSNA-1 self-assembly has a comparable effect on embryonic viability as the knockout strain. Our study provides molecular insights into SSNA-1's self-assembly and its role in microtubule binding and cell division regulation through centriole stability.

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Organizational Affiliation: 
• Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA.
Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, 20892, USA.
Institute for Protein Innovation, Boston, MA, 02115, USA.
Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA. [e-mail].
Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, 20892, USA. [e-mail].
Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA. [e-mail].
National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 32-mer - A32 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy, light scattering

Macromolecule Content 

• Total Structure Weight: 469.32 kDa 
• Atom Count: 26,528 
• Modeled Residue Count: 3,168 
• Deposited Residue Count: 3,968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sjogren's Syndrome Nuclear Autoantigen	A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	124	Caenorhabditis elegans	Mutation(s): 3  Gene Names: ssna-1, tag-261, CELE_T07A9.13, T07A9.13
UniProt
Find proteins for Q5F4U5 (Caenorhabditis elegans) Explore Q5F4U5  Go to UniProtKB:  Q5F4U5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.55 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207+SVN
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Agostini, L., Biertumpfel, C., Mizuno, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release