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- PDB-6lcr: Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lcr | |||||||||
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Title | Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP state | |||||||||
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![]() | LIPID TRANSPORT / P-type ATPase / lipid flippase | |||||||||
Function / homology | ![]() ATPase-coupled intramembrane lipid transporter activity / phospholipid transport / P-type phospholipid transporter / phospholipid translocation / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | He, Y. / Xu, J. / Wu, X. / Li, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of a P4-ATPase lipid flippase in lipid bilayers. Authors: Yilin He / Jinkun Xu / Xiaofei Wu / Long Li / ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.5 KB | Display | ![]() |
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PDB format | ![]() | 213.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0873MC ![]() 0872C ![]() 6lcpC 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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1 |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 175379.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0012810 / Production host: ![]() ![]() References: UniProt: G0S196, P-type phospholipid transporter |
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#2: Protein | Mass: 46452.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0052360 / Production host: ![]() ![]() |
-Sugars , 3 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 3 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/P5S.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/P5S.gif)
#5: Chemical | ChemComp-MG / |
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#6: Chemical | ChemComp-ACP / |
#7: Chemical | ChemComp-P5S / |
-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 |
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Sample preparation
Component | Name: Heterodimer of Dnf1-Cdc50 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K |
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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: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 57 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2397258 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272912 / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.88 Å2 | |||||||||||||||||||||||||||
Refine LS restraints |
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