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Yorodumi- EMDB-8948: PDB: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8948 | |||||||||
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Title | PDB: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ | |||||||||
Map data | afTMEM16 reconstituted into nanodiscs in the presence of Ca2 | |||||||||
Sample |
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Keywords | scramblase / Ca2+-activated / membrane-reorganization / LIPID TRANSPORT | |||||||||
Function / homology | Function and homology information phospholipid scramblase activity / cortical endoplasmic reticulum / phospholipid translocation / chloride channel activity / voltage-gated calcium channel activity / chloride transmembrane transport / monoatomic ion transmembrane transport / membrane Similarity search - Function | |||||||||
Biological species | Aspergillus fumigatus (mold) / Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.05 Å | |||||||||
Authors | Falzone ME / Accardi A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8948.map.gz | 54.1 MB | EMDB map data format | |
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Header (meta data) | emd-8948-v30.xml emd-8948.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8948_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_8948.png | 111.4 KB | ||
Masks | emd_8948_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-8948.cif.gz | 6.2 KB | ||
Others | emd_8948_additional.map.gz | 52.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8948 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8948 | HTTPS FTP |
-Related structure data
Related structure data | 6e0hMC 8931C 8959C 6dz7C 6e1oC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10239 (Title: afTMEM16/nanodisc complex in the presence of Ca2+ / Data size: 150.5 Data #1: motion corrected 2D micrographs from 50 frames of afTMEM16/nanodisc complex in the presdence of Ca2+ [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8948.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | afTMEM16 reconstituted into nanodiscs in the presence of Ca2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_8948_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: afTMEM16 Ca2 C1 unmasked map containing nanodisc density...
File | emd_8948_additional.map | ||||||||||||
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Annotation | afTMEM16 Ca2 C1 unmasked map containing nanodisc density used for membrane analysis | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : afTMEM16 reconstituted in nanodiscs in the presence of Ca2+
Entire | Name: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ |
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Components |
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-Supramolecule #1: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+
Supramolecule | Name: afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Aspergillus fumigatus (mold) |
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: Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 |
Molecular weight | Theoretical: 84.616859 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 presence of Ca2+ |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 69.97 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |