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Yorodumi- PDB-6lcp: Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lcp | |||||||||
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Title | Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state | |||||||||
Components |
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Keywords | LIPID TRANSPORT / P-type ATPase / lipid flippase | |||||||||
Function / homology | Function and homology information 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 | Chaetomium thermophilum (fungus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | He, Y. / Xu, J. / Wu, X. / Li, L. | |||||||||
Funding support | China, 1items
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Citation | Journal: Protein Cell / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lcp.cif.gz | 293.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lcp.ent.gz | 229.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lcp ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lcp | HTTPS FTP |
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-Related structure data
Related structure data | 0872MC 0873C 6lcrC 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: 175379.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0012810 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5425 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.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0052360 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5465 / References: UniProt: G0SDN0 |
-Sugars , 5 types, 6 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose |
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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 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 |
#6: 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 |
#11: Sugar |
-Non-polymers , 4 types, 5 molecules
#7: Chemical | ChemComp-MG / | ||
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#8: Chemical | ChemComp-BEF / | ||
#9: Chemical | #10: 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 |
-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: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5465 |
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 |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
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) |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2820251 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249694 / Num. of class averages: 1 / 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: 46.56 Å2 | |||||||||||||||||||||||||||
Refine LS restraints |
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