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Yorodumi- PDB-4cyl: Tomographic subvolume average of EFF-1 fusogen on extracellular v... -
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-Basic information
Entry | Database: PDB / ID: 4cyl | ||||||
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Title | Tomographic subvolume average of EFF-1 fusogen on extracellular vesicles | ||||||
Components | EFF-1A | ||||||
Keywords | CELL 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 / nematode pharyngeal muscle development / EFF-1 complex / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / syncytium formation by plasma membrane fusion / embryonic body morphogenesis ...nematode male tail mating organ morphogenesis / fusogenic activity / nematode pharyngeal muscle development / EFF-1 complex / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / syncytium formation by plasma membrane fusion / embryonic body morphogenesis / egg-laying behavior / cell-cell contact zone / locomotion / morphogenesis of an epithelium / kinase activity / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | CAENORHABDITIS ELEGANS (invertebrata) | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 22.2 Å | ||||||
Authors | Zeev-Ben-Mordehai, T. / Vasishtan, D. / Siebert, C.A. / Grunewald, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4cyl.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cyl.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cyl_validation.pdf.gz | 561.8 KB | Display | wwPDB validaton report |
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Full document | 4cyl_full_validation.pdf.gz | 579.5 KB | Display | |
Data in XML | 4cyl_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4cyl_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cyl ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cyl | HTTPS FTP |
-Related structure data
Related structure data | 2530MC 2531C 2532C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: EPITHELIAL FUSION FAILURE 1 (EFF-1) ISOFORM A ON EXTRACELLULAR VESICLES Type: COMPLEX |
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Buffer solution | Name: 25MM HEPES, 130MM NACL / pH: 7.4 / Details: 25MM HEPES, 130MM NACL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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 |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Mar 3, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 95000 X / Calibrated magnification: 78950 X / Nominal defocus max: 2500 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 85 K / Tilt angle max: 60 ° / Tilt angle min: -60 ° |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 78 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: 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 building | Protocol: FLEXIBLE FIT / Space: REAL Details: METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--FLEXIBLE FIT OF X-RAY STRUCTURE | ||||||||||||
Refinement | Highest resolution: 22.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 22.2 Å
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