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- EMDB-27152: Zebrafish MFSD2A isoform B in inward open ligand 2B conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-27152
TitleZebrafish MFSD2A isoform B in inward open ligand 2B conformation
Map dataSingle-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, filtered to local resolution.
Sample
  • Complex: Single-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, filtered to local resolution
    • Protein or peptide: Sodium-dependent lysophosphatidylcholine symporter 1-B
    • Protein or peptide: FAB light chain
    • Protein or peptide: FAB heavy chain
  • Ligand: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water
Keywordsomega-3 fatty acid / lipid transport / membrane protein / Fab
Function / homology
Function and homology information


Synthesis of PC / fatty acid transmembrane transporter activity / lysophospholipid translocation / lysophospholipid:sodium symporter activity / lysophospholipid transport / lipid transport across blood-brain barrier / establishment of blood-brain barrier / symporter activity / transcytosis / carbohydrate transport ...Synthesis of PC / fatty acid transmembrane transporter activity / lysophospholipid translocation / lysophospholipid:sodium symporter activity / lysophospholipid transport / lipid transport across blood-brain barrier / establishment of blood-brain barrier / symporter activity / transcytosis / carbohydrate transport / fatty acid transport / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Lactose permease-like / MFS/sugar transport protein / MFS transporter superfamily
Similarity search - Domain/homology
Sodium-dependent lysophosphatidylcholine symporter 1-B
Similarity search - Component
Biological speciesDanio rerio (zebrafish) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNguyen C / Lei HT / Lai LTF / Gallentino MJ / Mu X / Matthies D / Gonen T
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM136508 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)ZIA HD008998-01 United States
CitationJournal: Nat Commun / Year: 2023
Title: Lipid flipping in the omega-3 fatty-acid transporter.
Authors: Chi Nguyen / Hsiang-Ting Lei / Louis Tung Faat Lai / Marc J Gallenito / Xuelang Mu / Doreen Matthies / Tamir Gonen /
Abstract: Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions ...Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions to microcephaly. Mfsd2a transports long-chain unsaturated fatty-acids, including DHA and α-linolenic acid (ALA), that are attached to the zwitterionic lysophosphatidylcholine (LPC) headgroup. Even with the recently determined structures of Mfsd2a, the molecular details of how this transporter performs the energetically unfavorable task of translocating and flipping lysolipids across the lipid bilayer remains unclear. Here, we report five single-particle cryo-EM structures of Danio rerio Mfsd2a (drMfsd2a): in the inward-open conformation in the ligand-free state and displaying lipid-like densities modeled as ALA-LPC at four distinct positions. These Mfsd2a snapshots detail the flipping mechanism for lipid-LPC from outer to inner membrane leaflet and release for membrane integration on the cytoplasmic side. These results also map Mfsd2a mutants that disrupt lipid-LPC transport and are associated with disease.
History
DepositionMay 30, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27152.png

Downloads & links

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Map

FileDownload / File: emd_27152.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, filtered to local resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.2498744 - 5.2825003
Average (Standard dev.)0.0028015564 (±0.04539043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 324.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Single-particle cryo-EM map of MFSD2A isoform B from...

Fileemd_27152_additional_1.map
AnnotationSingle-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, unsharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Single-particle cryo-EM map of MFSD2A isoform B from...

Fileemd_27152_additional_2.map
AnnotationSingle-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, sharpened B-115.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Single-particle cryo-EM half map A of MFSD2A isoform...

Fileemd_27152_half_map_1.map
AnnotationSingle-particle cryo-EM half map A of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Single-particle cryo-EM half map B of MFSD2A isoform...

Fileemd_27152_half_map_2.map
AnnotationSingle-particle cryo-EM half map B of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Single-particle cryo-EM map of MFSD2A isoform B from zebrafish wi...

EntireName: Single-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, filtered to local resolution
Components
  • Complex: Single-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, filtered to local resolution
    • Protein or peptide: Sodium-dependent lysophosphatidylcholine symporter 1-B
    • Protein or peptide: FAB light chain
    • Protein or peptide: FAB heavy chain
  • Ligand: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: Single-particle cryo-EM map of MFSD2A isoform B from zebrafish wi...

SupramoleculeName: Single-particle cryo-EM map of MFSD2A isoform B from zebrafish with a Fab in the inward open ligand 2B conformation at an average resolution of 3.4 A, filtered to local resolution
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 56 KDa

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Macromolecule #1: Sodium-dependent lysophosphatidylcholine symporter 1-B

MacromoleculeName: Sodium-dependent lysophosphatidylcholine symporter 1-B
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 56.683965 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HENLYFQGGS DEVKLAKHET KSRLSVCSKL CYAIGGAPYQ ITGCAIGFFL QIYLLDVALL DPFYASIILF VGRAWDAVT DPTVGFLVSR TPWTRFGRMM PWIVLSTPFA VLCYFLIWYV PSVDQGKVVW YLIFYCCFQT LQTCFHVPYS A LTMFISTE ...String:
MHHHHHHHHH HENLYFQGGS DEVKLAKHET KSRLSVCSKL CYAIGGAPYQ ITGCAIGFFL QIYLLDVALL DPFYASIILF VGRAWDAVT DPTVGFLVSR TPWTRFGRMM PWIVLSTPFA VLCYFLIWYV PSVDQGKVVW YLIFYCCFQT LQTCFHVPYS A LTMFISTE QKERDSATAY RMTVEVLGTL IGTAIQGQIV GMANAPCIST EIDLQSTGLE VAPDVQITDP HVSLQDLRNA YM IASGVIC AIYVVCAVVL FLGVKEQKDT CRVRTEPMSF FQGICMVMGH GPYAKLVMGF LFTSLAFMLL EGNFALFCIY NLG FRNDFQ NVLLVIMLSA TLAIPFWQWF LTKFGKKTAV YIGTTSVVPF LISVVLVPSS LAVTYIASFA AGVSVAAAFL LPWS MLPDV VDDFKVQNPE SQGHEAIFYS FYVFFTKFAS GVSLGVSTLS LDFAGYVTRG CTQPGEVKLT LKILVSAAPI VLIII GLLI FISYPINEEK RQGNRKLLNE QREQ

UniProtKB: Sodium-dependent lysophosphatidylcholine symporter 1-B

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Macromolecule #2: FAB light chain

MacromoleculeName: FAB light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.674949 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: ALDINSPEAE KNAKGARARI TCNAGNQVGS AVAWFNQRPG DPASLLTYWA ATEKGVAGKQ SAQGASTKFS MSSAGPEAPS LSSYWCLLF EKGAFSFGGS KLNPREGAGP QASILPPSAD LNTSGGAAVV CFLPNWYGNI TVQWKTEAPQ SQANMSWPGQ A GANAAYAM ...String:
ALDINSPEAE KNAKGARARI TCNAGNQVGS AVAWFNQRPG DPASLLTYWA ATEKGVAGKQ SAQGASTKFS MSSAGPEAPS LSSYWCLLF EKGAFSFGGS KLNPREGAGP QASILPPSAD LNTSGGAAVV CFLPNWYGNI TVQWKTEAPQ SQANMSWPGQ A GANAAYAM AAVLAITKGD YGPGSFTCNA SNRGTGPFAM SLN

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Macromolecule #3: FAB heavy chain

MacromoleculeName: FAB heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.568018 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: ASKLELSGPA EPRGSKSAQI TCKAKGFPEA RFWVFWLFQR AAALDWPAAN FSGGPVQFES RFQGNASLKG SQAQANAELN IGALGSSTA TYRCGWKLAN GGFFPSWGGA NVNGAAGAKA PAVYPVEISG AGTGSVTLGC LVKGYNAKPN LTWPGASGAL T FPSELNGA ...String:
ASKLELSGPA EPRGSKSAQI TCKAKGFPEA RFWVFWLFQR AAALDWPAAN FSGGPVQFES RFQGNASLKG SQAQANAELN IGALGSSTA TYRCGWKLAN GGFFPSWGGA NVNGAAGAKA PAVYPVEISG AGTGSVTLGC LVKGYNAKPN LTWPGASGAL T FPSELNGA LWNLASAVTG SGFPSATCAV GFGAATDVDK KVAAA

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Macromolecule #4: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethox...

MacromoleculeName: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate
type: ligand / ID: 4 / Number of copies: 1 / Formula: ZGS
Molecular weightTheoretical: 518.644 Da
Chemical component information

ChemComp-ZGS:
[(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate

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Macromolecule #5: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 5 / Number of copies: 15 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMHEPES
150.0 mMNaCl
0.02 %DDM

Details: 50 mM HEPES (pH 8), 150 mM NaCl and 0.02% DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 86 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
Details: 400-mesh 1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for two times 60 seconds with a current of 15 mA in a PELCO easiGlow system. The cryo grids were produced ...Details: 400-mesh 1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for two times 60 seconds with a current of 15 mA in a PELCO easiGlow system. The cryo grids were produced using a Leica EM GP (Leica). The chamber was kept at 4 C and 95% humidity (86-91% measured). 3 microliter sample at 3 mg/ml was applied to a glow-discharged holey grid, blotted for 6 s, and plunge frozen into liquid ethane and stored in liquid nitrogen..
DetailsPurified 15A9 FAB fragment was incubated overnight at 4 C with MFSD2A at a 5:1 molar ratio. DrMFSD2A-15A9 complex was injected into the size exclusion column Superdex200 to separate the unbound FAB. The size exclusion column step was also used to exchange the buffer of the MFSD2A-FAB complex into 50 mM HEPES, 150 mM NaCl and 0.02% DDM. SDS-PAGE was used to pool peak fractions containing both MFSD2A and FAB, indicating complex formation. The pooled fractions containing MFSD2A-FAB were concentrated to 3 mg/ml using Amicon spin concentrator with a 30 kDa cutoff.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsCryo-EM grids were loaded into a 300 keV FEI Titan Krios cryo electron microscope (ThermoFisher Scientific, formerly FEI) at HHMI Janelia Reasearch Campus, Janelia Krios 1, equipped with a Cs corrector, and Gatan energy filter and K3 camera (Gatan Inc.). Movies of 50 frames with 1 e-/A2 per frame (50 e-/A2 total dose) were automatically recorded at a nominal magnification of 81,000x, corresponding to a physical pixel size of 0.844 A/px (superresolution pixel size 0.422 A/px) in CDS mode at a dose rate of 9.5 e-/px/s (~7.5 e-/px/s on the camera through the sample) and a defocus range of -0.5 to -1.8 micrometer using SerialEM. In total, 2,653 and 8,443 movies were collected in two separate imaging sessions, with the first dataset on a 400-mesh copper grid and the second on a 300-mesh UltrAuFoil gold grid.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 11096 / Average exposure time: 3.75 sec. / Average electron dose: 50.0 e/Å2
Details: Movies of 50 frames with 1 e-/A2 per frame (50 e-/A2 total dose) were automatically recorded at a nominal magnification of 81,000x, corresponding to a physical pixel size of 0.844 A/px ...Details: Movies of 50 frames with 1 e-/A2 per frame (50 e-/A2 total dose) were automatically recorded at a nominal magnification of 81,000x, corresponding to a physical pixel size of 0.844 A/px (superresolution pixel size 0.422 A/px) in CDS mode at a dose rate of 9.5 e-/px/s (~7.5 e-/px/s on the camera through the sample) and a defocus range of -0.5 to -1.8 mircometer using SerialEM. In total, 2,653 and 8,443 movies were collected in two separate imaging sessions, with the first dataset on a 400-mesh copper grid and the second on a 300-mesh UltrAuFoil gold grid.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMovies of 50 frames with 1 e-/A2 per frame (50 e-/A2 total dose) were automatically recorded at a nominal magnification of 81,000x, corresponding to a physical pixel size of 0.844 A/px (superresolution pixel size 0.422 A/px) in CDS mode at a dose rate of 9.5 e-/px/s (~7.5 e-/px/s on the camera through the sample) and a defocus range of -0.5 to -1.8 mircometer using SerialEM. In total, 2,653 and 8,443 movies were collected in two separate imaging sessions, with the first dataset on a 400-mesh copper grid and the second on a 300-mesh UltrAuFoil gold grid.
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 76700
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v3.3.2) / Details: SGD (stochastic gradient descent)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v3.3.2)
Details: Individual ligand densities were segmented and extracted with UCSF Chimera. Extracted ligand densities were then subtracted from the MFSD2A-FAB map, generating references with (1)3 ligands ...Details: Individual ligand densities were segmented and extracted with UCSF Chimera. Extracted ligand densities were then subtracted from the MFSD2A-FAB map, generating references with (1)3 ligands bound, (2) no ligand bound, (3) only ligand 1 bound, (4) only ligand 2 bound, and (5) only ligand 3 bound, respectively. These maps served as references for 3D classification without alignment, with a tight mask covering ligand binding sites included. To avoid reference bias and overfitting, individual particle subsets obtained from 3D classification were subjected to ab-initio reconstruction, followed by non-uniform refinement, resulting in maps at 3.3 A, 3.4 A, 3.3 A, 3.4 A, and 3.4 A, with local resolutions to up to 2.8 A (3-ligands, lower resolution), 2.8 A (ligand-free), 2.8 A (1A), 2.9 A (2B), and 2.9 A (3C), respectively
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. v3.3.2)
Details: Individual ligand densities were segmented and extracted with UCSF Chimera. Extracted ligand densities were then subtracted from the MFSD2A-FAB map, generating references with (1)3 ligands ...Details: Individual ligand densities were segmented and extracted with UCSF Chimera. Extracted ligand densities were then subtracted from the MFSD2A-FAB map, generating references with (1)3 ligands bound, (2) no ligand bound, (3) only ligand 1 bound, (4) only ligand 2 bound, and (5) only ligand 3 bound, respectively. These maps served as references for 3D classification without alignment, with a tight mask covering ligand binding sites included. To avoid reference bias and overfitting, individual particle subsets obtained from 3D classification were subjected to ab-initio reconstruction, followed by non-uniform refinement, resulting in maps at 3.3 A, 3.4 A, 3.3 A, 3.4 A, and 3.4 A, with local resolutions to up to 2.8 A (3-ligands, lower resolution), 2.8 A (ligand-free), 2.8 A (1A), 2.9 A (2B), and 2.9 A (3C), respectively
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7mjs


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8d2w:
Zebrafish MFSD2A isoform B in inward open ligand 2B conformation

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Atomic model buiding 2

Initial modelPDB ID:

7mjs


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 115
Output model

PDB-8d2w:
Zebrafish MFSD2A isoform B in inward open ligand 2B conformation

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