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Yorodumi- PDB-6lvf: Cryo-EM structure of the multiple peptide resistance factor (MprF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lvf | ||||||||||||
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Title | Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with one lysyl-phosphatidylglycerol molecule | ||||||||||||
Components | Low pH-inducible protein LpiA | ||||||||||||
Keywords | MEMBRANE PROTEIN / bacteria membrane protein | ||||||||||||
Function / homology | Function and homology information phosphatidylglycerol alanyltransferase activity / phospholipid homeostasis / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Rhizobium tropici CIAT 899 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Song, D.F. / Jiao, H.Z. / Liu, Z.F. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2021 Title: Phospholipid translocation captured in a bifunctional membrane protein MprF. Authors: Danfeng Song / Haizhan Jiao / Zhenfeng Liu / Abstract: As a large family of membrane proteins crucial for bacterial physiology and virulence, the Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate ...As a large family of membrane proteins crucial for bacterial physiology and virulence, the Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate aminoacyl phospholipids to the outer leaflets of bacterial membranes. The function of MprFs enables Staphylococcus aureus and other pathogenic bacteria to acquire resistance to daptomycin and cationic antimicrobial peptides. Here we present cryo-electron microscopy structures of MprF homodimer from Rhizobium tropici (RtMprF) at two different states in complex with lysyl-phosphatidylglycerol (LysPG). RtMprF contains a membrane-embedded lipid-flippase domain with two deep cavities opening toward the inner and outer leaflets of the membrane respectively. Intriguingly, a hook-shaped LysPG molecule is trapped inside the inner cavity with its head group bent toward the outer cavity which hosts a second phospholipid-binding site. Moreover, RtMprF exhibits multiple conformational states with the synthase domain adopting distinct positions relative to the flippase domain. Our results provide a detailed framework for understanding the mechanisms of MprF-mediated modification and translocation of phospholipids. | ||||||||||||
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 | 6lvf.cif.gz | 286 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lvf.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lvf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6lvf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6lvf_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 6lvf_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/6lvf ftp://data.pdbj.org/pub/pdb/validation_reports/lv/6lvf | HTTPS FTP |
-Related structure data
Related structure data | 0992MC 6lv0C 7duwC 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
#1: Protein | Mass: 96094.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium tropici CIAT 899 (bacteria) / Gene: lpiA, RTCIAT899_CH14740 / Production host: Escherichia coli (E. coli) / References: UniProt: L0LM43, UniProt: A0A6P1C618*PLUS #2: Chemical | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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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: bacterial membrane protein / Type: CELL Details: A recombinant protein from Rhizobium tropici expressed in Escherichia coli cells Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Source (natural) | Organism: Rhizobium tropici (bacteria) / Cellular location: Membrane | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The protein is reconstituted in lipid nanodiscs | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 291 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.2 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2921 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 887196 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160417 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient |