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Open data
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Basic information
Entry | Database: PDB / ID: 8hpl | ||||||
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Title | LpqY-SugABC in state 1 | ||||||
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![]() | TRANSPORT PROTEIN / Trehalose / ABC transporter / tuberculosis | ||||||
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: 4.29 Å | ||||||
![]() | Liang, J. / Yang, X. / Zhang, B. / Rao, Z. / Liu, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into trehalose capture and translocation by mycobacterial LpqY-SugABC. Authors: Jingxi Liang / Xiuna Yang / Tianyu Hu / Yan Gao / Qi Yang / Haitao Yang / Wei Peng / Xiaoting Zhou / Luke W Guddat / Bing Zhang / Zihe Rao / Fengjiang Liu / ![]() ![]() Abstract: The human pathogen, Mycobacterium tuberculosis (Mtb) relies heavily on trehalose for both survival and pathogenicity. The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the only ...The human pathogen, Mycobacterium tuberculosis (Mtb) relies heavily on trehalose for both survival and pathogenicity. The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the only trehalose import pathway in Mtb. Conformational dynamics of ABC transporters is an important feature to explain how they operate, but experimental structures are determined in a static environment. Therefore, a detailed transport mechanism cannot be elucidated because there is a lack of intermediate structures. Here, we used single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the Mycobacterium smegmatis (M. smegmatis) trehalose-specific importer LpqY-SugABC complex in five different conformations. These structures have been classified and reconstructed from a single cryo-EM dataset. This study allows a comprehensive understanding of the trehalose recycling mechanism in Mycobacteria and also demonstrates the potential of single-particle cryo-EM to explore the dynamic structures of other ABC transporters and molecular machines. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.2 KB | Display | ![]() |
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PDB format | ![]() | 224.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34932MC ![]() 8hpmC ![]() 8hpnC ![]() 8hprC ![]() 8hpsC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 2 types, 2 molecules AE
#1: Protein | Mass: 32739.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: sugA, MSMEI_4933 Production host: ![]() References: UniProt: I7G6S2 |
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#4: Protein | Mass: 50183.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MSMEG_5061 Production host: ![]() References: UniProt: A0R2C3 |
-ABC transporter, ... , 2 types, 3 molecules BCD
#2: Protein | Mass: 29839.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MSMEG_5059 Production host: ![]() References: UniProt: A0R2C1 |
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#3: Protein | Mass: 43702.625 Da / Num. of mol.: 2 / Mutation: E164N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MSMEG_5058 Production host: ![]() References: UniProt: A0R2C0 |
-Sugars / Non-polymers , 2 types, 3 molecules ![](data/chem/img/ATP.gif)
#5: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Chemical |
-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: Trehalose-specific importer LpqY-SugABC complex / Type: COMPLEX / Entity ID: #3, #1-#2, #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 / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49940 / Symmetry type: POINT | ||||||||||||||||||||||||
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