8HPM | pdb_00008hpm

LpqY-SugABC in state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into trehalose capture and translocation by mycobacterial LpqY-SugABC.

Liang, J.Yang, X.Hu, T.Gao, Y.Yang, Q.Yang, H.Peng, W.Zhou, X.Guddat, L.W.Zhang, B.Rao, Z.Liu, F.

(2023) Structure 31: 1158-1165.e3

  • DOI: https://doi.org/10.1016/j.str.2023.07.014
  • Primary Citation Related Structures: 
    8HPL, 8HPM, 8HPN, 8HPR, 8HPS

  • PubMed 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 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.


  • Organizational Affiliation
    • State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 201.52 kDa 
  • Atom Count: 12,803 
  • Modeled Residue Count: 1,758 
  • Deposited Residue Count: 1,860 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC sugar transporter, permease component305Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: sugAMSMEI_4933
Membrane Entity: Yes 
UniProt
Find proteins for A0R2C2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R2C2 
Go to UniProtKB:  A0R2C2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R2C2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC transporter, permease protein SugB278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_5059
Membrane Entity: Yes 
UniProt
Find proteins for A0R2C1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R2C1 
Go to UniProtKB:  A0R2C1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R2C1
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC transporter, ATP-binding protein SugC
C, D
406Mycolicibacterium smegmatis MC2 155Mutation(s): 1 
Gene Names: MSMEG_5058
Membrane Entity: Yes 
UniProt
Find proteins for A0R2C0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R2C0 
Go to UniProtKB:  A0R2C0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R2C0
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacterial extracellular solute-binding protein465Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_5061
Membrane Entity: Yes 
UniProt
Find proteins for A0R2C3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R2C3 
Go to UniProtKB:  A0R2C3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R2C3
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranoseF [auth G]2N/A
Glycosylation Resources
GlyTouCan: G92130SN
GlyCosmos: G92130SN

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200983

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection, Structure summary