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- PDB-12zn: Septin tetrameric complex from Caenorhabditis elegans by Cryo-EM -

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Basic information

Entry
Database: PDB / ID: 12zn
TitleSeptin tetrameric complex from Caenorhabditis elegans by Cryo-EM
Components(Septin) x 2
KeywordsCELL CYCLE / GTPase / Cytoskeleton component
Function / homology
Function and homology information


egg-laying behavior / septin complex / cytoskeleton-dependent cytokinesis / septin ring / post-embryonic development / locomotion / cell division site / cleavage furrow / intracellular protein localization / microtubule cytoskeleton ...egg-laying behavior / septin complex / cytoskeleton-dependent cytokinesis / septin ring / post-embryonic development / locomotion / cell division site / cleavage furrow / intracellular protein localization / microtubule cytoskeleton / midbody / molecular adaptor activity / cytoskeleton / GTPase activity / GTP binding
Similarity search - Function
Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Septin / Septin
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsSaladino, G.C.R. / Ciol, H. / Mendonca, D.C. / Furtado, A.A. / Pereira, H.M. / Klaholz, B. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)20/02897-1 Brazil
CitationJournal: J Mol Biol / Year: 2026
Title: Cryo-EM Structure of the C. Elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.
Authors: Giovanna Christe Dos Reis Saladino / Heloísa Ciol / Deborah Cezar Mendonça / Adriano Alves Furtado / Humberto D'Muniz Pereira / Bruno P Klaholz / Ana Paula Ulian Araujo / Richard Charles Garratt /
Abstract: Septins are cytoskeletal proteins that assemble into hetero-oligomeric complexes, which polymerize into filaments to regulate many cellular processes, including cytokinesis and membrane remodeling. ...Septins are cytoskeletal proteins that assemble into hetero-oligomeric complexes, which polymerize into filaments to regulate many cellular processes, including cytokinesis and membrane remodeling. In Caenorhabditis elegans, the core septin complex is a tetramer composed of two copies each of two different subunits, UNC-59 and UNC-61. Historically, low-resolution models suggested a subunit order of UNC-59-UNC-61-UNC-61-UNC-59 for the tetramer. However, this arrangement contradicted the positional conservation of septins observed in other species. Using cryo-EM, we obtained a structure for the tetramer with a global resolution of 2.7 Å, definitively establishing the subunit order to be UNC-61-UNC-59-UNC-59-UNC-61. This places UNC-59 at the center of the particle where it forms a homodimeric G-interface, confirming it to be a positional ortholog of human SEPT7. This arrangement is further supported by mutational/biophysical analyses. Despite the stability of the tetramer, the complex failed to polymerize into filaments in vitro, which we attribute to the structural instability of the terminal UNC-61 G-interfaces. Our results suggest that post-translational modifications or specific cellular factors may be required to initiate higher-order assembly in C. elegans. Furthermore, our structure reveals that while UNC-59 possesses key characteristics of the SEPT7 group, it also features unique structural adaptations that may be related to the unique arrangement of the C. elegans complex. We demonstrate that the previous misidentification of the subunit order within the tetramer likely stemmed from N-terminal domain swapping, reinforcing the importance of high-resolution structural studies for understanding the evolutionary history and the diversity of septins.
History
DepositionApr 24, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septin
B: Septin
C: Septin
D: Septin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,7576
Polymers216,8704
Non-polymers8862
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Septin


Mass: 53135.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-61, CELE_Y50E8A.4, Y50E8A.4 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9U277
#2: Protein Septin


Mass: 55299.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-59, CELE_W09C5.2, W09C5.2 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9U334
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - UNC-61)
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.20931 MDa / Experimental value: YES
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta DE3 / Plasmid: pETDuet
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HClC4H11NO31
2500 mMSodium chlorideNaCl1
35 mMMagnesium chlorideMgCl21
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5998

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.0particle selection
2EPUimage acquisition
7PHENIX1.20.1_4487model fittingDock in map
11cryoSPARC4.7.0classification
12cryoSPARC4.7.03D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 5900000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198470 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDChain-IDChain residue rangeDetails (eV)Source nameType
11A29-315UNC-59AlphaFoldin silico model
21B82-363UNC-61AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00257229
ELECTRON MICROSCOPYf_angle_d0.49529723
ELECTRON MICROSCOPYf_chiral_restr0.04221102
ELECTRON MICROSCOPYf_plane_restr0.00361226
ELECTRON MICROSCOPYf_dihedral_angle_d8.4759957

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