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Open data
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Basic information
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Title | Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs | |||||||||
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![]() | bacteria / outer membrane / phospholipid / lipid asymmetry / membrane protein / protein complex structure / channel / LIPID TRANSPORT | |||||||||
Function / homology | ![]() intermembrane phospholipid transfer / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity / receptor-mediated virion attachment to host cell / DNA damage response / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||
![]() | Yeow J / Luo M / Chng SS | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Authors: Jiang Yeow / Min Luo / Shu-Sin Chng / ![]() Abstract: The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the ...The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 62.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.4 KB 24.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 105 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i8rMC ![]() 8i8xC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 0.834 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Outer membrane complex of OmpC-MlaA with periplasmic MlaC reconst...
Entire | Name: Outer membrane complex of OmpC-MlaA with periplasmic MlaC reconstituted in MSP2N2 nanodiscs |
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Components |
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-Supramolecule #1: Outer membrane complex of OmpC-MlaA with periplasmic MlaC reconst...
Supramolecule | Name: Outer membrane complex of OmpC-MlaA with periplasmic MlaC reconstituted in MSP2N2 nanodiscs type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Outer membrane complex of OmpC with disulfide-trapped MlaA and MlaC reconstituted in Escherichia coli polar lipids and MSP2N2 nanodiscs |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 28 KDa |
-Supramolecule #2: Outer membrane porin C
Supramolecule | Name: Outer membrane porin C / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: OmpC |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Intermembrane phospholipid transport system lipoprotein MlaA
Supramolecule | Name: Intermembrane phospholipid transport system lipoprotein MlaA type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: MlaA |
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-Macromolecule #1: Outer membrane porin C
Macromolecule | Name: Outer membrane porin C / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.336242 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AEVYNKDGNK LDLYGKVDGL HYFSDNKDVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGNPSGE G FTSGVTNN ...String: AEVYNKDGNK LDLYGKVDGL HYFSDNKDVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGNPSGE G FTSGVTNN GRDALRQNGD GVGGSITYDY EGFGIGGAIS SSKRTDAQNT AAYIGNGDRA ETYTGGLKYD ANNIYLAAQY TQ TYNATRV GSLGWANKAQ NFEAVAQYQF DFGLRPSLAY LQSKGKNLGR GYDDEDILKY VDVGATYYFN KNMSTYVDYK INL LDDNQF TRDAGINTDN IVALGLVYQF UniProtKB: Outer membrane porin C |
-Macromolecule #2: Intermembrane phospholipid transport system lipoprotein MlaA
Macromolecule | Name: Intermembrane phospholipid transport system lipoprotein MlaA type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.298336 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: CASSGTDQQG RSDPLEGFNR TMYNFNFNVL DPYIVRPVAV AWRDYVPQPA RNGLSNFTGN LEEPAVMVNY FLQGDPYQGM VHFTRFFLN TILGMGGFID VAGMANPKLQ RTEPHRFGST LGHYGVGYGP YVQLPFYGSF TLRDDGGDMA DGFYPVLSWL T WPMSVGKW ...String: CASSGTDQQG RSDPLEGFNR TMYNFNFNVL DPYIVRPVAV AWRDYVPQPA RNGLSNFTGN LEEPAVMVNY FLQGDPYQGM VHFTRFFLN TILGMGGFID VAGMANPKLQ RTEPHRFGST LGHYGVGYGP YVQLPFYGSF TLRDDGGDMA DGFYPVLSWL T WPMSVGKW TLEGIETRAQ LLDSDGLLRC SSDPYIMVRE AYFQRHDFIA NGGELKPQEN PNAQAIQDDL KDIDSE UniProtKB: Intermembrane phospholipid transport system lipoprotein MlaA |
-Macromolecule #3: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(...
Macromolecule | Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3- ...Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid type: ligand / ID: 3 / Number of copies: 3 / Formula: KDL |
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Molecular weight | Theoretical: 2.238718 KDa |
Chemical component information | ![]() ChemComp-KDL: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 12 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl) | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Tridiem 4K / Energy filter - Slit width: 20 eV Details: Gatan GIF post-column energy filter operated in zero-loss mode |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6018 / Average exposure time: 5.99 sec. / Average electron dose: 90.0 e/Å2 Details: Images were collected in movie-mode at 50 frames per image |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Details | Building of the high-resolution structures of OmpC-MlaA was done via approximate fitting using the OmpC-MlaA crystal structure (PDB 5NUP) as rigid bodies into the density in Chimera, followed by refinement in COOT. | |||||||||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 88 / Target criteria: Cross-correlation coefficient | |||||||||||||||
Output model | ![]() PDB-8i8r: |