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Yorodumi- PDB-7ky6: Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ky6 | ||||||
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Title | Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state | ||||||
Components |
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Keywords | TRANSLOCASE / P4 ATPase / Phosphatidylcholine Flippases | ||||||
Function / homology | Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / phospholipid translocation / Cation transport ATPase (P-type) / membrane => GO:0016020 / LEM3 isoform 1 / : Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Bai, L. / You, Q. / Jain, B.K. / Duan, H.D. / Kovach, A. / Graham, T.R. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ky6.cif.gz | 256 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ky6.ent.gz | 202.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ky6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ky6_validation.pdf.gz | 907.4 KB | Display | wwPDB validaton report |
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Full document | 7ky6_full_validation.pdf.gz | 935.2 KB | Display | |
Data in XML | 7ky6_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 7ky6_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/7ky6 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/7ky6 | HTTPS FTP |
-Related structure data
Related structure data | 23069MC 7ky5C 7ky7C 7ky8C 7ky9C 7kyaC 7kybC 7kycC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 178000.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: DNF1, YER166W, SYGP-ORF7 / Production host: Saccharomyces cerevisiae S288C (yeast) / Strain (production host): ATCC 204508 / S288c References: UniProt: P32660, P-type phospholipid transporter |
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#2: Protein | Mass: 47490.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c Gene: LEM3, GI526_G0004759, PACBIOSEQ_LOCUS5272, PACBIOSEQ_LOCUS5307, SCNYR20_0008001200, SCP684_0008000800 Production host: Saccharomyces cerevisiae S288C (yeast) / Strain (production host): ATCC 204508 / S288c / References: UniProt: A0A6A5Q828 |
-Sugars , 3 types, 5 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
-Non-polymers , 1 types, 1 molecules
#5: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Source (recombinant) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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 |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
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: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473761 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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