[English] 日本語
![](img/lk-miru.gif)
- PDB-7ky9: Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ky9 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state | ||||||
![]() |
| ||||||
![]() | TRANSLOCASE / P4 ATPase / Phosphatidylcholine Flippases | ||||||
Function / homology | ![]() regulation of vacuole organization / glycosylceramide flippase activity / mating projection tip membrane / aminophospholipid translocation / Ion transport by P-type ATPases / aminophospholipid flippase activity / phosphatidylserine flippase activity / ceramide translocation / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity ...regulation of vacuole organization / glycosylceramide flippase activity / mating projection tip membrane / aminophospholipid translocation / Ion transport by P-type ATPases / aminophospholipid flippase activity / phosphatidylserine flippase activity / ceramide translocation / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / cellular bud neck / P-type phospholipid transporter / phospholipid translocation / establishment or maintenance of cell polarity / cell periphery / endocytosis / protein transport / cell surface receptor signaling pathway / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 Å | ||||||
![]() | Bai, L. / You, Q. / Jain, B.K. / Duan, H.D. / Kovach, A. / Graham, T.R. / Li, H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Transport mechanism of P4 ATPase phosphatidylcholine flippases. Authors: Lin Bai / Qinglong You / Bhawik K Jain / H Diessel Duan / Amanda Kovach / Todd R Graham / Huilin Li / ![]() ![]() 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 ...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 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. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 251.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 197.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 23072MC ![]() 7ky5C ![]() 7ky6C ![]() 7ky7C ![]() 7ky8C ![]() 7kyaC ![]() 7kybC ![]() 7kycC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 182834.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: DNF2, YDR093W, YD8557.01 / Production host: ![]() ![]() References: UniProt: Q12675, P-type phospholipid transporter |
---|---|
#2: Protein | Mass: 47490.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: LEM3, BRE3, ROS3, YNL323W, N0333 / Production host: ![]() ![]() |
-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#3: Polysaccharide | alpha-D-mannopyranose-(3-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
---|---|---|---|---|---|
#4: Polysaccharide | #8: Sugar | ChemComp-NAG / | #9: Sugar | ChemComp-MAN / | |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
#5: Chemical | ChemComp-ADP / |
---|---|
#6: Chemical | ChemComp-ALF / |
#7: Chemical |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Source (recombinant) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266218 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|