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- EMDB-0992: Cryo-EM structure of the multiple peptide resistance factor (MprF... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0992 | ||||||||||||
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Title | Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with one lysyl-phosphatidylglycerol molecule | ||||||||||||
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![]() | bacteria membrane protein / MEMBRANE PROTEIN | ||||||||||||
Function / homology | : / phosphatidylglycerol alanyltransferase activity / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / phospholipid homeostasis / Acyl-CoA N-acyltransferase / plasma membrane / Bifunctional lysylphosphatidylglycerol flippase/synthetase MprF / : ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Song DF / Jiao HZ | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.8 KB | Display | ![]() |
Images | ![]() | 23.4 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lvfMC ![]() 6lv0C ![]() 7duwC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : bacterial membrane protein
Entire | Name: bacterial membrane protein |
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Components |
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-Supramolecule #1: bacterial membrane protein
Supramolecule | Name: bacterial membrane protein / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: A recombinant protein from Rhizobium tropici expressed in Escherichia coli cells |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Low pH-inducible protein LpiA
Macromolecule | Name: Low pH-inducible protein LpiA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 96.094672 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSSPIDLESA DEELEERGGI VGLLNRYRAL IVAVLTVAVF CIAAYAIYDL TTEVRYDDVV HALTTTKISS VLLALLFTGL SFASLIFYD QNALEYIGKR LPFPHVALTS FSAYAVGNTA GFGALSAGAI RYRAYTRLGL SPDDITRVIA FVTLAFGLGL A SVGAMALL ...String: MSSPIDLESA DEELEERGGI VGLLNRYRAL IVAVLTVAVF CIAAYAIYDL TTEVRYDDVV HALTTTKISS VLLALLFTGL SFASLIFYD QNALEYIGKR LPFPHVALTS FSAYAVGNTA GFGALSAGAI RYRAYTRLGL SPDDITRVIA FVTLAFGLGL A SVGAMALL VIADEIGPLI SVDGLWLRLI AIAILAALAF VVYAGRNGRE VRIGPVAVRL PDSRTWSRQF LVTAFDIAAS AS VLYVLLP ETSIGWPGFF AIYAIAVGLG VLSHVPAGFG VFETIIIAWL GSSVNEDAVL SSLVLYRVIY NVIPLVIAIA AIS VAELRR FVDHPVASSM RRIGARLMPQ LLSAFALLLG MMLVFSSVTP TPDHNLIVLS DYLPLSLVES AHFLSSLLGL AIIV AARGL SQRLDGAWWV STFSALFALF FSLLKAIAIV EAGLLAFFVF SLVVSRRLFK RPASLLNQTL TAGWLTAIAV VCIGA IVVL FFVYRDVGYS NELWWQFEFA DEAPRGLRAA LGISIVSSAI AIFSLLRPAT KRPEPVSDDA VARAVEIVRK QGVADA NLV RMGDKSIMFS EKGDAFIMYG KQGRSWIALF DPVGPRQALP DLIWRFVETA RAAGCRSVFY QISPALLSYC ADAGLRA FK LGELAVVNLA NFELKGGKWA NLRQTASRAV RDGLEFAVIE PQDIPDVLDQ LAHVSDTWLA DHNAKEKSFS LGAFDPDY V CSQPVGVLKK DGKIVAFANI LMTETKEEGS VDLMRFSPDA PKGSMDFLFV QILEYLKGEG FQRFNLGMAP LSGMSRRES APVWDRVGGT VFEHGERFYN FKGLRAFKSK FHPEWQPRYL AVSGGVSPMI ALMDATFLIG GGLKGVVRKK LAAALEHHHH HH UniProtKB: UNIPROTKB: L0LM43 |
-Macromolecule #2: [(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl)hexanoyl]oxy-2-oxi...
Macromolecule | Name: [(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate type: ligand / ID: 2 / Number of copies: 2 / Formula: EV9 |
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Molecular weight | Theoretical: 851.142 Da |
Chemical component information | ![]() ChemComp-EV9: |
-Macromolecule #3: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Macromolecule | Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 3 / Number of copies: 2 / Formula: LHG |
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Molecular weight | Theoretical: 722.97 Da |
Chemical component information | ![]() ChemComp-LHG: |
-Macromolecule #4: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
Macromolecule | Name: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE type: ligand / ID: 4 / Number of copies: 2 / Formula: PGT |
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Molecular weight | Theoretical: 751.023 Da |
Chemical component information | ![]() ChemComp-PGT: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | The protein is reconstituted in lipid nanodiscs |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 2921 / Average exposure time: 5.2 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-6lvf: |