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Open data
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Basic information
Entry | Database: PDB / ID: 7arh | ||||||
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Title | LolCDE in complex with lipoprotein | ||||||
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![]() | PROTEIN TRANSPORT / LolCDE / lipoprotein / lipoprotein transporter / lipoprotein sorting and transport | ||||||
Function / homology | ![]() lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / 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 / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Tang, X.D. / Chang, S.H. / Zhang, K. / Wang, T. / Luo, Q.H. / Qiao, W. / Wang, C. / Zhang, Z.B. / Zhang, Z.Y. / Zhu, X.F. ...Tang, X.D. / Chang, S.H. / Zhang, K. / Wang, T. / Luo, Q.H. / Qiao, W. / Wang, C. / Zhang, Z.B. / Zhang, Z.Y. / Zhu, X.F. / Dong, C.J. / Zhang, X. / Dong, H.H. | ||||||
![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 218.7 KB | Display | ![]() |
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PDB format | ![]() | 180.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11882MC ![]() 7ariC ![]() 7arjC ![]() 7arkC ![]() 7arlC ![]() 7armC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Lipoprotein-releasing system ... , 2 types, 3 molecules EFD
#2: Protein | Mass: 45385.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: lolE, ycfW, b1118, JW1104 / Production host: ![]() ![]() |
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#3: Protein | Mass: 26576.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: lolD, ycfV, b1117, JW5162 / Production host: ![]() ![]() References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
-Protein / Protein/peptide , 2 types, 2 molecules CV
#1: Protein | Mass: 43295.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: lolC, FAZ83_19940 / Production host: ![]() ![]() |
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#4: Protein/peptide | Mass: 1079.206 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/Z41.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/PLM.gif)
#5: Chemical | ChemComp-Z41 / ( |
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#6: Chemical | ChemComp-PLM / |
-Details
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 |
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Sample preparation
Component | Name: LolCDE in complex with a lipoprotein / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.8 / Details: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl and 0.05% LMNG |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 95 % |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||
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EM software | Name: RELION / Category: classification | ||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49517 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building |
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