7KY8 | pdb_00007ky8

Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ATP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7KY8

This is version 1.2 of the entry. See complete history

Literature

Transport mechanism of P4 ATPase phosphatidylcholine flippases.

Bai, L.You, Q.Jain, B.K.Duan, H.D.Kovach, A.Graham, T.R.Li, H.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.62163
  • Primary Citation Related Structures: 
    7KY5, 7KY6, 7KY7, 7KY8, 7KY9, 7KYA, 7KYB, 7KYC

  • PubMed Abstract: 

    The P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases-such as the yeast Drs2 and human ATP8A1-have recently been reported. However, a substrate-binding site on the cytosolic side has not been found, and the transport mechanisms of P4 ATPases with other substrates are unknown. Here, we report structures of the S. cerevisiae Dnf1-Lem3 and Dnf2-Lem3 complexes. We captured substrate phosphatidylcholine molecules on both the exoplasmic and cytosolic sides and found that they have similar structures. Unexpectedly, Lem3 contributes to substrate binding. The conformational transitions of these phosphatidylcholine transporters match those of the phosphatidylserine transporters, suggesting a conserved mechanism among P4 ATPases. Dnf1/Dnf2 have a unique P domain helix-turn-helix insertion that is important for function. Therefore, P4 ATPases may have retained an overall transport mechanism while evolving distinct features for different lipid substrates.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 235.21 kDa 
  • Atom Count: 10,520 
  • Modeled Residue Count: 1,274 
  • Deposited Residue Count: 2,026 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholipid-transporting ATPase DNF21,612Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DNF2YDR093WYD8557.01
EC: 7.6.2.1
Membrane Entity: Yes 
UniProt
Find proteins for Q12675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12675 
Go to UniProtKB:  Q12675
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12675
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alkylphosphocholine resistance protein LEM3414Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEM3BRE3ROS3YNL323WN0333
Membrane Entity: Yes 
UniProt
Find proteins for P42838 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P42838 
Go to UniProtKB:  P42838
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42838
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P42838-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, F
2N/AN-Glycosylation
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(3-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N/AN-Glycosylation

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP

Query on ACP



Download:Ideal Coordinates CCD File
L [auth A]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
O [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
M [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA231466 to H.L. and GM107978 to T.R.G.

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-05-21
    Changes: Data collection