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- EMDB-47147: Cryo-EM structure of SSNA-1(R18E/R20E/Q98E) filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-47147
TitleCryo-EM structure of SSNA-1(R18E/R20E/Q98E) filaments
Map dataauto-sharpened map used for model building
Sample
  • Complex: self-assembled SSNA-1 filaments
    • Protein or peptide: Sjogren's Syndrome Nuclear Autoantigen
KeywordsSSNA1 / DIP13 / NA14 / microtubules / centriole / centrosome / mitotic spindle / cytoskeleton / coiled-coil / CELL CYCLE
Function / homologySjogren's Syndrome Nuclear Autoantigen
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
Methodhelical reconstruction / cryo EM / Resolution: 4.55 Å
AuthorsAgostini L / Biertumpfel C / Mizuno N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into SSNA1 self-assembly and its microtubule binding for centriole maintenance.
Authors: Lorenzo Agostini / Jason A Pfister / Nirakar Basnet / Jienyu Ding / Rui Zhang / Christian Biertümpfel / Kevin F O'Connell / Naoko Mizuno /
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 ...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.
History
DepositionSep 27, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47147.png

Downloads & links

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Map

FileDownload / File: emd_47147.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationauto-sharpened map used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 256 pix.
= 421.888 Å		1.65 Å/pix.
x 256 pix.
= 421.888 Å		1.65 Å/pix.
x 256 pix.
= 421.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.15
Minimum - Maximum-7.5536385 - 15.001493999999999
Average (Standard dev.)-0.000000000004843 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 421.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47147_msk_1.map
Projections & Slices
AxesZYX

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Additional map: unsharpened map from cryosparc refinement

Fileemd_47147_additional_1.map
Annotationunsharpened map from cryosparc refinement
Projections & Slices
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Half map: half map A from cryosparc

Fileemd_47147_half_map_1.map
Annotationhalf map A from cryosparc
Projections & Slices
AxesZYX

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Half map: half map B from cryosparc

Fileemd_47147_half_map_2.map
Annotationhalf map B from cryosparc
Projections & Slices
AxesZYX

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Sample components

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Entire : self-assembled SSNA-1 filaments

EntireName: self-assembled SSNA-1 filaments
Components
  • Complex: self-assembled SSNA-1 filaments
    • Protein or peptide: Sjogren's Syndrome Nuclear Autoantigen

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Supramolecule #1: self-assembled SSNA-1 filaments

SupramoleculeName: self-assembled SSNA-1 filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 20 kDa/nm

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Macromolecule #1: Sjogren's Syndrome Nuclear Autoantigen

MacromoleculeName: Sjogren's Syndrome Nuclear Autoantigen / type: protein_or_peptide / ID: 1 / Number of copies: 32 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 14.666279 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGKHHHHHHG SLEVLFQGPM SSRSTGSFDE ISQYIQELEE ERRLTESSIR KMEKEKSDLN EKIDELTTRK CSVDARLQAE NERAERQDR GLKEAETTYA KLVESQKTLV DFVRKEYEDT KHQKY

UniProtKB: Sjogren's Syndrome Nuclear Autoantigen

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaH2PO4sodium phosphate
10.0 mMNaOHsodium hydroxide
150.0 mMNaClsodium chloride
10.0 %HOCH2CH(OH)CH2OHglycerol
1.0 mMHSCH2CH(OH)CH(OH)CH2SHDTT
0.1 %C14H28O6n-octyl-beta-D-glucopyranoside

Details: 50 mM sodium phosphate buffer-NaOH pH 7.5, 150 mM NaCl, 10% (v/v) glycerol, 1 mM DTT, 0.1% (v/v) n-octyl-beta-D-glucopyranoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 35.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: LEICA EM GP
Details: After 1 min incubation at room temperature, the grid was manually blotted on the side of the grid with filter paper (Whatman Grade 1, Cytiva #1001-055) and blotted again with 4 uL of a ...Details: After 1 min incubation at room temperature, the grid was manually blotted on the side of the grid with filter paper (Whatman Grade 1, Cytiva #1001-055) and blotted again with 4 uL of a solution containing lysis buffer supplemented with 0.1 %(v/v) n-octyl-beta-D-glucopyranoside (beta-OG, Anatrace #O311). The grid was then transferred to an EM GP2 plunger (Leica) with a chamber temperature of 15degC, maximal humidity, incubated for 1 min, blotted with Grade 595 filter paper (Ted Pella #47000-200) for 6 s and vitrified in liquid ethane..
DetailsSSNA-1(R18E/R20E/Q98E) was dialyzed overnight at 4degC against buffer to grow filaments. 5 ul sample at a final concentration of 0.1 mg/mL was applied to glow discharged Quantifoil grids R2/1.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsDetails: pixel size 0.412
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8390 / Average exposure time: 2.0 sec. / Average electron dose: 40.84 e/Å2 / Details: pixel size 0.412
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 112.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 45 °
Applied symmetry - Helical parameters - Axial symmetry: C8 (8 fold cyclic)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Details: no helical parameters used / Number images used: 80664
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: NONE
Segment selectionNumber selected: 888099 / Software - Name: cryoSPARC (ver. 4.5.3)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 265.8
Output model

PDB-9dsm:
Cryo-EM structure of SSNA-1(R18E/R20E/Q98E) filaments

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