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- PDB-7rxa: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rxa | ||||||
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Title | afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+ | ||||||
![]() | afTMEM16 lipid scramblase | ||||||
![]() | LIPID TRANSPORT / TMEM16 / lipid scrambling | ||||||
Function / homology | ![]() phospholipid scramblase activity / cortical endoplasmic reticulum / phospholipid translocation / chloride channel activity / voltage-gated calcium channel activity / monoatomic ion transmembrane transport / chloride transmembrane transport / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
![]() | Feng, Z. / Accardi, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: TMEM16 scramblases thin the membrane to enable lipid scrambling. Authors: Maria E Falzone / Zhang Feng / Omar E Alvarenga / Yangang Pan / ByoungCheol Lee / Xiaolu Cheng / Eva Fortea / Simon Scheuring / Alessio Accardi / ![]() ![]() Abstract: TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets ...TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets through a membrane-spanning hydrophilic groove. Direct information on lipid-groove interactions is lacking. We report the 2.3 Å resolution cryogenic electron microscopy structure of the nanodisc-reconstituted Ca-bound afTMEM16 scramblase showing how rearrangement of individual lipids at the open pathway results in pronounced membrane thinning. Only the groove's intracellular vestibule contacts lipids, and mutagenesis suggests scrambling does not require specific protein-lipid interactions with the extracellular vestibule. We find scrambling can occur outside a closed groove in thinner membranes and is inhibited in thicker membranes, despite an open pathway. Our results show afTMEM16 thins the membrane to enable scrambling and that an open hydrophilic pathway is not a structural requirement to allow rapid transbilayer movement of lipids. This mechanism could be extended to other scramblases lacking a hydrophilic groove. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.2 KB | Display | ![]() |
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PDB format | ![]() | 162.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 60.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24726MC ![]() 7rwjC ![]() 7rx2C ![]() 7rx3C ![]() 7rxbC ![]() 7rxgC ![]() 7rxhC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 84514.812 Da / Num. of mol.: 2 / Mutation: D511A, E514A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUA_4G02970 / Production host: ![]() ![]() #2: Chemical | ChemComp-PGW / ( Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+ Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 42.18 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155902 / Symmetry type: POINT |