[English] 日本語
Yorodumi
- PDB-4cyl: Tomographic subvolume average of EFF-1 fusogen on extracellular v... -

+
Open data


ID or keywords:

Loading...

-
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 / chordate pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / vulval development / cell-cell fusion / syncytium formation by plasma membrane fusion / egg-laying behavior ...nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / chordate pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / vulval development / cell-cell fusion / syncytium formation by plasma membrane fusion / egg-laying behavior / embryonic body morphogenesis / cell-cell contact zone / locomotion / morphogenesis of an epithelium / kinase activity / phosphorylation / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2530
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EFF-1A


Theoretical massNumber of molelcules
Total (without water)74,4971
Polymers74,4971
Non-polymers00
Water0
1


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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy / 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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more