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- EMDB-41482: nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold pro... -
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Open data
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Basic information
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Title | nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (short TM6) | |||||||||
![]() | Primary map used for model building | |||||||||
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![]() | membrane protein / lipid scramblase / TMEM16 / LIPID TRANSPORT | |||||||||
Function / homology | ![]() cortical endoplasmic reticulum / chloride channel activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
![]() | Feng Z / Accardi A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of closed groove scrambling by a TMEM16 protein. Authors: Zhang Feng / Omar E Alvarenga / Alessio Accardi / ![]() Abstract: Activation of Ca-dependent TMEM16 scramblases induces phosphatidylserine externalization, a key step in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by ...Activation of Ca-dependent TMEM16 scramblases induces phosphatidylserine externalization, a key step in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by deforming the membrane near a hydrophilic groove and that Ca dependence arises from the different association of lipids with an open or closed groove. However, the molecular rearrangements underlying groove opening and how lipids reorganize outside the closed groove remain unknown. Here we directly visualize how lipids associate at the closed groove of Ca-bound fungal nhTMEM16 in nanodiscs using cryo-EM. Functional experiments pinpoint lipid-protein interaction sites critical for closed groove scrambling. Structural and functional analyses suggest groove opening entails the sequential appearance of two π-helical turns in the groove-lining TM6 helix and identify critical rearrangements. Finally, we show that the choice of scaffold protein and lipids affects the conformations of nhTMEM16 and their distribution, highlighting a key role of these factors in cryo-EM structure determination. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 90.4 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() ![]() | 48.3 MB 48.5 MB 48.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tprMC ![]() 8toiC ![]() 8tokC ![]() 8tolC ![]() 8tpmC ![]() 8tpnC ![]() 8tpoC ![]() 8tppC ![]() 8tpqC ![]() 8tpsC ![]() 8tptC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Primary map used for model building | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map, used to assist model building
File | emd_41482_additional_1.map | ||||||||||||
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Annotation | unsharpened map, used to assist model building | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap2
File | emd_41482_half_map_1.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap1
File | emd_41482_half_map_2.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dimeric lipid scramblase nhTMEM16
Entire | Name: Dimeric lipid scramblase nhTMEM16 |
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Components |
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-Supramolecule #1: Dimeric lipid scramblase nhTMEM16
Supramolecule | Name: Dimeric lipid scramblase nhTMEM16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Lipid scramblase nhTMEM16
Macromolecule | Name: Lipid scramblase nhTMEM16 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 83.320094 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPSNLKDFSQ PGSGQESNFG VDFVIHYKVP AAERDEAEAG FVQLIRALTT VGLATEVRHG ENESLLVFVK VASPDLFAKQ VYRARLGDW LHGVRVSAPH NDIAQALQDE PVVEAERLRL IYLMITKPHN EGGAGVTPTN AKWKHVESIF PLHSHSFNKE W IKKWSSKY ...String: GPSNLKDFSQ PGSGQESNFG VDFVIHYKVP AAERDEAEAG FVQLIRALTT VGLATEVRHG ENESLLVFVK VASPDLFAKQ VYRARLGDW LHGVRVSAPH NDIAQALQDE PVVEAERLRL IYLMITKPHN EGGAGVTPTN AKWKHVESIF PLHSHSFNKE W IKKWSSKY TLEQTDIDNI RDKFGESVAF YFAFLRSYFR FLVIPSAFGF GAWLLLGQFS YLYALLCGLW SVVFFEYWKK QE VDLAVQW GVRGVSSIQQ SRPEFEWEHE AEDPITGEPV KVYPPMKRVK TQLLQIPFAL ACVVALGALI VTCNSLEVFI NEV YSGPGK QYLGFLPTIF LVIGTPTISG VLMGAAEKLN AMENYATVDA HDAALIQKQF VLNFMTSYMA LFFTAFVYIP FGHI LHPFL NFWRATAQTL TFSEKELPTR EFQINPARIS NQMFYFTVTP QIVNFATEVV VPYIKQQAFQ KAKQLKSGSK VQEDH EEEA EFLQRVREEC TLEEYDVSGD YREMVMQFGY VAMFSVAWPL AACCFLVNNW VELRSDALKI AISSRRPIPW RTDSIG PWL TALSFLSWLG SITSSAIVYL CSNSKNGTQG EASPLKAWGL LLSILFAEHF YLVVQLAVRF VLSKLDSPGL QKERKER FQ TKKRLLQENL GQDAAEEAAA PGIEHSEKIT REALEEEARQ ASIRGHGTPE EMFWQRQRGM QETIEIGRRM IEQQLAAG K NGKKSAPAVP SEKASA UniProtKB: Plasma membrane channel protein |
-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: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...
Macromolecule | Name: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate type: ligand / ID: 3 / Number of copies: 4 / Formula: PGW |
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Molecular weight | Theoretical: 749.007 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 11976 / Average exposure time: 2.0 sec. / Average electron dose: 59.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |