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- EMDB-24726: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-24726
TitleafTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+
Map dataUsed for the building of the protein part and some lipids in the model
Sample
  • Complex: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+
    • Protein or peptide: afTMEM16 lipid scramblase
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
KeywordsTMEM16 / lipid scrambling / 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
: / Alpha-beta plait domain in TMEM16 lipid scramblase / Anoctamin / : / Calcium-activated chloride channel
Similarity search - Domain/homology
Plasma membrane channel protein (Aqy1), putative
Similarity search - Component
Biological speciesAspergillus fumigatus (mold) / Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsFeng Z / Accardi A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106717 United States
CitationJournal: Nat Commun / Year: 2022
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
DepositionAug 22, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24726.png

Downloads & links

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Map

FileDownload / File: emd_24726.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUsed for the building of the protein part and some lipids in the model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.09654853 - 0.17713065
Average (Standard dev.)0.00007869814 (±0.004409548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Used for the building of some lipids in the model

Fileemd_24726_additional_1.map
AnnotationUsed for the building of some lipids in the model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+

EntireName: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+
Components
  • Complex: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+
    • Protein or peptide: afTMEM16 lipid scramblase
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+

SupramoleculeName: afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aspergillus fumigatus (mold)

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Macromolecule #1: afTMEM16 lipid scramblase

MacromoleculeName: afTMEM16 lipid scramblase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163
Molecular weightTheoretical: 84.514812 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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 DYDVTDALRA 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

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Macromolecule #2: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 8 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155902
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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