+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11886 | |||||||||
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Title | LolCDE in complex with lipoprotein and ADP | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / membrane => GO:0016020 ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Tang XD / Chang SH / Zhang K / Wang T / Luo QH / Qiao W / Wang C / Shen CR / Zhang ZB / Zhang ZY ...Tang XD / Chang SH / Zhang K / Wang T / Luo QH / Qiao W / Wang C / Shen CR / Zhang ZB / Zhang ZY / Zhu XF / Wei XW / Dong CJ / Zhang X / Dong HH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structural basis for bacterial lipoprotein relocation by the transporter LolCDE. Authors: Xiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing ...Authors: Xiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong / Abstract: Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the ...Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the inner membrane, lipoproteins must be transported to the outer membrane through the Lol pathway mediated by the ATP-binding cassette transporter LolCDE in the inner membrane via an unknown mechanism. Here, we report cryo-EM structures of Escherichia coli LolCDE in apo, lipoprotein-bound, LolA-bound, ADP-bound and AMP-PNP-bound states at a resolution of 3.2-3.8 Å, covering the complete lipoprotein transport cycle. Mutagenesis and in vivo viability assays verify features of the structures and reveal functional residues and structural characteristics of LolCDE. The results provide insights into the mechanisms of sorting and transport of outer-membrane lipoproteins and may guide the development of novel therapies against multidrug-resistant Gram-negative bacteria. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11886.map.gz | 25 MB | EMDB map data format | |
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Header (meta data) | emd-11886-v30.xml emd-11886.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_11886.png | 52.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11886 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11886 | HTTPS FTP |
-Related structure data
Related structure data | 7arlMC 7arhC 7ariC 7arjC 7arkC 7armC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11886.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : LolCDE in complex with lipoprotein and ADP
+Supramolecule #1: LolCDE in complex with lipoprotein and ADP
+Supramolecule #2: Lipoprotein-releasing complex
+Supramolecule #3: LPP
+Macromolecule #1: Lipoprotein-releasing ABC transporter permease subunit LolC
+Macromolecule #2: Lipoprotein-releasing system transmembrane protein LolE
+Macromolecule #3: Lipoprotein-releasing system ATP-binding protein LolD
+Macromolecule #4: LPP
+Macromolecule #5: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
+Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: PALMITIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.8 / Details: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl and 0.05% LMNG |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % |
Details | LolCDE in complex with lipoprotein and ADP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2756322 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164632 |