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- PDB-7cag: Mycobacterium smegmatis LpqY-SugABC complex in the catalytic inte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cag | |||||||||
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Title | Mycobacterium smegmatis LpqY-SugABC complex in the catalytic intermediate state | |||||||||
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![]() | TRANSPORT PROTEIN / ABC transporter / Lipoprotein / Trehalose / Trehalose-specific importer / Mycobacteria | |||||||||
Function / homology | ![]() : / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å | |||||||||
![]() | Liu, F. / Liang, J. / Zhang, B. / Gao, Y. / Yang, X. / Hu, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of trehalose recycling by the ABC transporter LpqY-SugABC. Authors: Fengjiang Liu / Jingxi Liang / Bing Zhang / Yan Gao / Xiuna Yang / Tianyu Hu / Haitao Yang / Wenqing Xu / Luke W Guddat / Zihe Rao / ![]() ![]() Abstract: In bacteria, adenosine 5'-triphosphate (ATP)-binding cassette (ABC) importers are essential for the uptake of nutrients including the nonreducing disaccharide trehalose, a metabolite that is crucial ...In bacteria, adenosine 5'-triphosphate (ATP)-binding cassette (ABC) importers are essential for the uptake of nutrients including the nonreducing disaccharide trehalose, a metabolite that is crucial for the survival and virulence of several human pathogens including SugABC is an ABC transporter that translocates trehalose from the periplasmic lipoprotein LpqY into the cytoplasm of mycobacteria. Here, we report four high-resolution cryo-electron microscopy structures of the mycobacterial LpqY-SugABC complex to reveal how it binds and passes trehalose through the membrane to the cytoplasm. A unique feature observed in this system is the initial mode of capture of the trehalose at the LpqY interface. Uptake is achieved by a pivotal rotation of LpqY relative to SugABC, moving from an open and accessible conformation to a clamped conformation upon trehalose binding. These findings enrich our understanding as to how ABC transporters facilitate substrate transport across the membrane in Gram-positive bacteria. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.2 KB | Display | ![]() |
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PDB format | ![]() | 237.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30330MC ![]() 7cadC ![]() 7caeC ![]() 7cafC 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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Components
-Protein , 2 types, 2 molecules EA
#1: Protein | Mass: 50183.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5061 Production host: ![]() References: UniProt: A0R2C3 |
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#2: Protein | Mass: 32739.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: sugA, MSMEI_4933 Production host: ![]() References: UniProt: I7G6S2, UniProt: A0R2C2*PLUS |
-ABC transporter, ... , 2 types, 3 molecules BCD
#3: Protein | Mass: 29839.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5059 Production host: ![]() References: UniProt: A0R2C1 |
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#4: Protein | Mass: 43702.625 Da / Num. of mol.: 2 / Mutation: E164Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5058 Production host: ![]() References: UniProt: A0R2C0 |
-Sugars , 1 types, 1 molecules
#5: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose |
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-Non-polymers , 2 types, 4 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ATP.gif)
#6: Chemical | #7: Chemical | |
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-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: Mycobacterium smegmatis LpqY-SugABC complex in the catalytic intermediate state Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120290 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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