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- EMDB-8959: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8959 | |||||||||
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Title | afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and ceramide 24:0 | |||||||||
![]() | afTMEM16 in the presence of Ca2+ and ceramide 24:0 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Falzone ME / Accardi A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of Ca-dependent activation and lipid transport by a TMEM16 scramblase. Authors: Maria E Falzone / Jan Rheinberger / Byoung-Cheol Lee / Thasin Peyear / Linda Sasset / Ashleigh M Raczkowski / Edward T Eng / Annarita Di Lorenzo / Olaf S Andersen / Crina M Nimigean / Alessio Accardi / ![]() ![]() Abstract: The lipid distribution of plasma membranes of eukaryotic cells is asymmetric and phospholipid scramblases disrupt this asymmetry by mediating the rapid, nonselective transport of lipids down their ...The lipid distribution of plasma membranes of eukaryotic cells is asymmetric and phospholipid scramblases disrupt this asymmetry by mediating the rapid, nonselective transport of lipids down their concentration gradients. As a result, phosphatidylserine is exposed to the outer leaflet of membrane, an important step in extracellular signaling networks controlling processes such as apoptosis, blood coagulation, membrane fusion and repair. Several TMEM16 family members have been identified as Ca-activated scramblases, but the mechanisms underlying their Ca-dependent gating and their effects on the surrounding lipid bilayer remain poorly understood. Here, we describe three high-resolution cryo-electron microscopy structures of a fungal scramblase from , afTMEM16, reconstituted in lipid nanodiscs. These structures reveal that Ca-dependent activation of the scramblase entails global rearrangement of the transmembrane and cytosolic domains. These structures, together with functional experiments, suggest that activation of the protein thins the membrane near the transport pathway to facilitate rapid transbilayer lipid movement. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 58.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9 KB | Display | ![]() |
Images | ![]() | 123.2 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e1oMC ![]() 8931C ![]() 8948C ![]() 6dz7C ![]() 6e0hC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 113.8 Data #1: motion corrected 2D micrographs from 45 frames of afTMEM16/nanodisc complex in the presence of Ca2+ and 5 mol% ceramide 24:0 [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | afTMEM16 in the presence of Ca2+ and ceramide 24:0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0961 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and c...
Entire | Name: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and ceramide 24:0 |
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Components |
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-Supramolecule #1: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and c...
Supramolecule | Name: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and ceramide 24:0 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 168 kDa/nm |
-Macromolecule #1: Plasma membrane channel protein (Aqy1), putative
Macromolecule | Name: Plasma membrane channel protein (Aqy1), putative / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 |
Molecular weight | Theoretical: 84.616859 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MAFNPAPKAV QENHHVDYVI RFNYGDIDTP EAIKKFEVLL LELSEVGLQT EVRQGDENSL FVFVRAASKK KLKRAVYQSR VRDWLYGVR NTEPEPASSA KPQSEAERLL VIYHLITVPK AEGGAGITPR HGEWKNVDAI FPLHDEETNR QCMREWSKKT F LSTEDLDR ...String: MAFNPAPKAV QENHHVDYVI RFNYGDIDTP EAIKKFEVLL LELSEVGLQT EVRQGDENSL FVFVRAASKK KLKRAVYQSR VRDWLYGVR NTEPEPASSA KPQSEAERLL VIYHLITVPK AEGGAGITPR HGEWKNVDAI FPLHDEETNR QCMREWSKKT F LSTEDLDR IRNTFGEHVG FYFAFLQSYF RFLMFPAAFG FSCWLLLGSF SIIYTVVNCL WCIVFIEYWK RQEEDLSCRW QT KGVSAVH EKRAEFKPEK EIRDESTGEV RGVFPATKRM YRQLLQVPFA LLAAVALGAI IATCFAIEIF ISEVYNGPLK GYL VFIPTI LVSALIPTMS AVLLTVATKL NDYENYETQD AYKVALTQKI FVVNFITSYL PIILTAFVYV PFASRIVPYL DVFH LTVRP FVSKEHAIKA RTEFSINPDR LRKQVIYFTV TAQIVGFALE TIVPFVKQRV FREYKEYTKK QHAKAEPGNG AGEKK TVSL GDDEDEARFL TRVRNEAELE DYDVTDDLRE MCIQFGYLAL FSPVWPLVPV SFLINNWVEL RSDFFKICVE CKRPWP QRA DTIGPWLDSL GFLSWVGSIT SSALVYMFSN GHEGPNGEPT TIRCWALLLT IFFSEHLYLI VRYAVRSALA KLEPPNT RR ERIERFMMRK RYLDTVLSAE SDDDADEVKG VVSSIPPSEI TRESLEQDAR DWSKQGTDPT ERFWMRQRGW KESAEVGL S LITKAKGDET KKQQ UniProtKB: Plasma membrane channel protein (Aqy1), putative |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: DODECANE
Macromolecule | Name: DODECANE / type: ligand / ID: 3 / Number of copies: 8 / Formula: D12 |
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Molecular weight | Theoretical: 170.335 Da |
Chemical component information | ![]() ChemComp-D12: |
-Macromolecule #4: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 4 / Number of copies: 2 / Formula: D10 |
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Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ![]() ChemComp-D10: |
-Macromolecule #5: Octadecane
Macromolecule | Name: Octadecane / type: ligand / ID: 5 / Number of copies: 2 / Formula: 8K6 |
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Molecular weight | Theoretical: 254.494 Da |
Chemical component information | ![]() ChemComp-8K6: |
-Macromolecule #6: HEXANE
Macromolecule | Name: HEXANE / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEX |
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Molecular weight | Theoretical: 86.175 Da |
Chemical component information | ![]() ChemComp-HEX: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 7 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV |
Details | afTMEM16 reconstituted in nanodiscs in the absence of Ca2+ |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 62.75 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |