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- PDB-4cyl: Tomographic subvolume average of EFF-1 fusogen on extracellular v... -

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Basic information

Entry
Database: PDB / ID: 4cyl
TitleTomographic subvolume average of EFF-1 fusogen on extracellular vesicles
ComponentsEFF-1A
KeywordsCELL ADHESION / CELL-CELL FUSION / EXTRACELLULAR FUSION / MEMBRANE FUSION / PRE-FUSION STATE
Function / homology
Function and homology information


nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / nematode pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / egg-laying behavior / syncytium formation by plasma membrane fusion ...nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / nematode pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / egg-laying behavior / syncytium formation by plasma membrane fusion / embryonic body morphogenesis / cell-cell contact zone / locomotion / morphogenesis of an epithelium / kinase activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cell-cell fusogen EFF/AFF / Cell-cell fusogen EFF/AFF, domain 3 / Type I membrane glycoproteins cell-cell fusogen
Similarity search - Domain/homology
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 22.2 Å
AuthorsZeev-Ben-Mordehai, T. / Vasishtan, D. / Siebert, C.A. / Grunewald, K.
CitationJournal: Nat Commun / Year: 2014
Title: The full-length cell-cell fusogen EFF-1 is monomeric and upright on the membrane.
Authors: Tzviya Zeev-Ben-Mordehai / Daven Vasishtan / C Alistair Siebert / Kay Grünewald /
Abstract: Fusogens are membrane proteins that remodel lipid bilayers to facilitate membrane merging. Although several fusogen ectodomain structures have been solved, structural information on full-length, ...Fusogens are membrane proteins that remodel lipid bilayers to facilitate membrane merging. Although several fusogen ectodomain structures have been solved, structural information on full-length, natively membrane-anchored fusogens is scarce. Here we present the electron cryo microscopy three-dimensional reconstruction of the Caenorhabditis elegans epithelial fusion failure 1 (EFF-1) protein natively anchored in cell-derived membrane vesicles. This reveals a membrane protruding, asymmetric, elongated monomer. Flexible fitting of a protomer of the EFF-1 crystal structure, which is homologous to viral class-II fusion proteins, shows that EFF-1 has a hairpin monomeric conformation before fusion. These structural insights, when combined with our observations of membrane-merging intermediates between vesicles, enable us to propose a model for EFF-1 mediated fusion. This process, involving identical proteins on both membranes to be fused, follows a mechanism that shares features of SNARE-mediated fusion while using the structural building blocks of the unilaterally acting class-II viral fusion proteins.
History
DepositionApr 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • EMDB-2530
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Structure viewerMolecule:
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Assembly

Deposited unit
A: EFF-1A


Theoretical massNumber of molelcules
Total (without water)74,4971
Polymers74,4971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein EFF-1A / EPITHELIAL FUSION FAILURE 1 / ISOFORM A


Mass: 74497.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEINS ON EXTRACELLULAR VESICLES / Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Plasmid: PCAGGS / Cell line (production host): BHK 21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: G5ECA1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: EPITHELIAL FUSION FAILURE 1 (EFF-1) ISOFORM A ON EXTRACELLULAR VESICLES
Type: COMPLEX
Buffer solutionName: 25MM HEPES, 130MM NACL / pH: 7.4 / Details: 25MM HEPES, 130MM NACL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, TEMPERATURE- 77, INSTRUMENT- HOMEMADE PLUNGER, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Mar 3, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 95000 X / Calibrated magnification: 78950 X / Nominal defocus max: 2500 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 85 K / Tilt angle max: 60 ° / Tilt angle min: -60 °
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 78
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2PEET3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SUBTOMOGRAM AVERAGING / Resolution: 22.2 Å / Num. of particles: 801 / Nominal pixel size: 3.8 Å / Actual pixel size: 3.8 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2530. (DEPOSITION ID: 12175).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--FLEXIBLE FIT OF X-RAY STRUCTURE
RefinementHighest resolution: 22.2 Å
Refinement stepCycle: LAST / Highest resolution: 22.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 0 0 3644

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