8D2V

Zebrafish MFSD2A isoform B in inward open ligand 1B conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lipid flipping in the omega-3 fatty-acid transporter.

Nguyen, C.Lei, H.T.Lai, L.T.F.Gallenito, M.J.Mu, X.Matthies, D.Gonen, T.

(2023) Nat Commun 14: 2571-2571

  • DOI: https://doi.org/10.1038/s41467-023-37702-7
  • Primary Citation of Related Structures:  
    8D2S, 8D2T, 8D2U, 8D2V, 8D2W, 8D2X

  • PubMed 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 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.


  • Organizational Affiliation

    Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent lysophosphatidylcholine symporter 1-B508Danio rerioMutation(s): 3 
Gene Names: mfsd2abnls1bsi:ch211-194e15.3si:ch211-210b19.5
Membrane Entity: Yes 
UniProt
Find proteins for Q6DEJ6 (Danio rerio)
Explore Q6DEJ6 
Go to UniProtKB:  Q6DEJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DEJ6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FAB light chain201Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FAB heavy chain203Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZGS (Subject of Investigation/LOI)
Query on ZGS

Download Ideal Coordinates CCD File 
D [auth A][(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
C26 H49 N O7 P
WKQNRCYKYCKESD-YVHLTTHBSA-O
LMT
Query on LMT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.3.2
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41-GM136508
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesZIA HD008998-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Refinement description, Structure summary