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- EMDB-76887: Septin tetrameric complex from Caenorhabditis elegans by Cryo-EM -

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Basic information

Entry
Database: EMDB / ID: EMD-76887
TitleSeptin tetrameric complex from Caenorhabditis elegans by Cryo-EM
Map dataMap sharpening
Sample
  • Complex: Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - UNC-61)
    • Protein or peptide: Septin
    • Protein or peptide: Septin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsGTPase / Cytoskeleton component / CELL CYCLE
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
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsSaladino GCR / Ciol H / Mendonca DC / Furtado AA / Pereira HM / Klaholz B / Araujo APU / Garratt RC
Funding support Brazil, 1 items
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, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76887.png

Downloads & links

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Map

FileDownload / File: emd_76887.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpening
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.248 Å		0.73 Å/pix.
x 512 pix.
= 373.248 Å		0.73 Å/pix.
x 512 pix.
= 373.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.6158867 - 2.9726505
Average (Standard dev.)-0.00004917435 (±0.026513994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76887_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_76887_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_76887_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - ...

EntireName: Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - UNC-61)
Components
  • Complex: Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - UNC-61)
    • Protein or peptide: Septin
    • Protein or peptide: Septin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - ...

SupramoleculeName: Heterotetramer of C. elegans septins (UNC-61 - UNC-59 - UNC-59 - UNC-61)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 209.31 KDa

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Macromolecule #1: Septin

MacromoleculeName: Septin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 53.135703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMSDIEHKLQ HLPPHQPPPP VPHHHQNQPT HNNTTTISSA TSSINTTTTS KKPTIAAPTA PSPIKSLSDH TGRVMQLNGH VGFDSLPHQ LVKKAVEAGF QFNLMCVGET GTGKTTLIES LFNMKLDFEP CNHELKTVEL RTCTKDVAEG GIRVKLRLVE T AGFGDQLD ...String:
MMSDIEHKLQ HLPPHQPPPP VPHHHQNQPT HNNTTTISSA TSSINTTTTS KKPTIAAPTA PSPIKSLSDH TGRVMQLNGH VGFDSLPHQ LVKKAVEAGF QFNLMCVGET GTGKTTLIES LFNMKLDFEP CNHELKTVEL RTCTKDVAEG GIRVKLRLVE T AGFGDQLD KDKSAKVIVD YLESQFETYL QEELKPRRML QYFNDSRIHA CLYFISPTGH GLKALDLVTL RELAKRVNVI PV IAKSDTT CKDELLRFKA KILSELKSQK IDIYTFPTDD ETVSTTNKEM NKSVPFAVVG SIDFVKKENG QMVRARQYPW GIV EVENES HCDFVKLREA LLRTNVDEMR QRTHESLYEN YRRDRLRQMK IGDGETGPKI IEKLAQKHRE HQDEFSRREL TLRE EFQKK LDVTEGDMRK VEEGLAARER EVHENYNREA SKLDMEIRQL TEERMKLMTK VSKKLRK

UniProtKB: Septin

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Macromolecule #2: Septin

MacromoleculeName: Septin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 55.299492 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGMHHHHHHE NLYFQGSQDP SSRTANSSSR NDESLRTGQH KENPNYWGFA NFPNQVFRRA VKNGFDFTLM VVGRSGLGKS TFINTLFLA EINNLNEKES APTHPHPSTV RVEEKLVKLV ENSVSLNLTL VDTPGFGDAV NNSKCWEPIV NYVESKFFEQ F CEETRIDR ...String:
MGMHHHHHHE NLYFQGSQDP SSRTANSSSR NDESLRTGQH KENPNYWGFA NFPNQVFRRA VKNGFDFTLM VVGRSGLGKS TFINTLFLA EINNLNEKES APTHPHPSTV RVEEKLVKLV ENSVSLNLTL VDTPGFGDAV NNSKCWEPIV NYVESKFFEQ F CEETRIDR GEKIVDKCVH LCLYFIEPSG HGLKPIDIEL MKHLHGRVNI VPVISKADCL TRDELLRFKK QIVKDAETAE IK LYKFPEL EDPYTDKVAI EKLRKALPFA IIGSNMLKEK DGKKIRYREY PWGTVEVENM QHNDFLTLRD MIIRTNLIDM IDV TRNVHY ENFRFRQMEG LPKNEKNRDP FTHLEEERRQ KEQDLDEKRN TLEKVFTEKT SARKKRSDER MSALEELEQQ NKQK IDAKR AEIIRLRHEI SELKNGNLTS SQTSLAMYNE NNHSQNSTLN STTKSSPPPT SATSSSSGTM KKRMGGLGLF NRN

UniProtKB: Septin

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris-HCl
500.0 mMNaClSodium chloride
5.0 mMMgCl2Magnesium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 5998 / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
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

Particle selectionNumber selected: 5900000
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 198470
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, residue_range: 29-315, source_name: AlphaFold, initial_model_type: in silico modelUNC-59
chain_id: B, residue_range: 82-363, source_name: AlphaFold, initial_model_type: in silico modelUNC-61
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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