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- PDB-7rd8: Structure of the S. cerevisiae P4B ATPase lipid flippase in the E... -
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Basic information
Entry | Database: PDB / ID: 7rd8 | ||||||
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Title | Structure of the S. cerevisiae P4B ATPase lipid flippase in the E1-ATP state | ||||||
![]() | Probable phospholipid-transporting ATPase NEO1 | ||||||
![]() | TRANSLOCASE / P4B ATPase lipid flippase | ||||||
Function / homology | ![]() lysophosphatidylserine flippase activity / trans-Golgi network membrane organization / Ion transport by P-type ATPases / phosphatidylserine flippase activity / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / phosphatidylethanolamine flippase activity / vacuole organization / P-type phospholipid transporter / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...lysophosphatidylserine flippase activity / trans-Golgi network membrane organization / Ion transport by P-type ATPases / phosphatidylserine flippase activity / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / phosphatidylethanolamine flippase activity / vacuole organization / P-type phospholipid transporter / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phospholipid translocation / trans-Golgi network / endocytosis / protein transport / late endosome / endosome membrane / endosome / Golgi membrane / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.64 Å | ||||||
![]() | Bai, L. / Jain, B.K. / You, Q. / Duan, H.D. / Graham, T.R. / Li, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of the P4B ATPase lipid flippase activity. Authors: Lin Bai / Bhawik K Jain / Qinglong You / H Diessel Duan / Mehmet Takar / Todd R Graham / Huilin Li / ![]() ![]() Abstract: P4 ATPases are lipid flippases that are phylogenetically grouped into P4A, P4B and P4C clades. The P4A ATPases are heterodimers composed of a catalytic α-subunit and accessory β-subunit, and the ...P4 ATPases are lipid flippases that are phylogenetically grouped into P4A, P4B and P4C clades. The P4A ATPases are heterodimers composed of a catalytic α-subunit and accessory β-subunit, and the structures of several heterodimeric flippases have been reported. The S. cerevisiae Neo1 and its orthologs represent the P4B ATPases, which function as monomeric flippases without a β-subunit. It has been unclear whether monomeric flippases retain the architecture and transport mechanism of the dimeric flippases. Here we report the structure of a P4B ATPase, Neo1, in its E1-ATP, E2P-transition, and E2P states. The structure reveals a conserved architecture as well as highly similar functional intermediate states relative to dimeric flippases. Consistently, structure-guided mutagenesis of residues in the proposed substrate translocation path disrupted Neo1's ability to establish membrane asymmetry. These observations indicate that evolutionarily distant P4 ATPases use a structurally conserved mechanism for substrate transport. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 181.4 KB | Display | ![]() |
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PDB format | ![]() | 138.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 854 KB | Display | ![]() |
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Full document | ![]() | 866.2 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24415MC ![]() 7rd6C ![]() 7rd7C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 130363.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NEO1, YIL048W / Production host: ![]() ![]() References: UniProt: P40527, P-type phospholipid transporter |
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#2: Chemical | ChemComp-ACP / |
#3: Chemical | ChemComp-MG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: P4B ATPase lipid flippase in the E1-ATP state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 264891 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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