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Yorodumi- PDB-7f7f: Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f7f | |||||||||
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Title | Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with beryllium fluoride (resting state) | |||||||||
Components |
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Keywords | LIPID TRANSPORT / P4-ATPases | |||||||||
Function / homology | Function and homology information regulation of vacuole organization / aminophospholipid translocation / phospholipid-translocating ATPase complex / phospholipid translocation / cell surface receptor signaling pathway / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å | |||||||||
Authors | Xu, J. / He, Y. / Wu, X. / Li, L. | |||||||||
Funding support | China, 1items
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Citation | Journal: Cell Rep / Year: 2022 Title: Conformational changes of a phosphatidylcholine flippase in lipid membranes. Authors: Jinkun Xu / Yilin He / Xiaofei Wu / Long Li / Abstract: Type 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid ...Type 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid flipping. It is unclear how the active flipping states of P4-ATPases are regulated in the lipid membranes, especially for phosphatidylcholine (PC)-flipping P4-ATPases whose substrate, PC, is a substantial component of membranes. Here, we report the cryoelectron microscopy structures of a yeast PC-flipping P4-ATPase, Dnf1, in lipid environments. In native yeast lipids, Dnf1 adopts a conformation in which the lipid flipping pathway is disrupted. Only when the lipid composition is changed can Dnf1 be captured in the active conformations that enable lipid flipping. These results suggest that, in the native membrane, Dnf1 may stay in an idle conformation that is unable to support the trans-membrane movement of lipids. Dnf1 may have altered conformational preferences in membranes with different lipid compositions. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f7f.cif.gz | 287 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f7f.ent.gz | 221.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f7f_validation.pdf.gz | 890.4 KB | Display | wwPDB validaton report |
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Full document | 7f7f_full_validation.pdf.gz | 905 KB | Display | |
Data in XML | 7f7f_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 7f7f_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f7f ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f7f | HTTPS FTP |
-Related structure data
Related structure data | 31487MC 7drxC 7dshC 7dsiC 7whvC 7whwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: DNF1, YER166W, SYGP-ORF7 / Production host: Saccharomyces cerevisiae S288C (yeast) 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 S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: LEM3, BRE3, ROS3, YNL323W, N0333 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P42838 |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | 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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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: Dnf1_Lem3 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 8 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212294 / Symmetry type: POINT | ||||||||||||||||||||||||
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