7CAG

Mycobacterium smegmatis LpqY-SugABC complex in the catalytic intermediate state

• PDB DOI:  https://doi.org/10.2210/pdb7CAG/pdb
• EM Map EMD-30330: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2020-06-08 Released: 2020-12-02 
• Deposition Author(s): Liu, F., Liang, J., Zhang, B., Gao, Y., Yang, X., Hu, T.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of trehalose recycling by the ABC transporter LpqY-SugABC.

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

(2020) Sci Adv 6

• PubMed: 33127676 
• DOI: https://doi.org/10.1126/sciadv.abb9833
• Primary Citation of Related Structures:  
  7CAD, 7CAE, 7CAF, 7CAG


• PubMed 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 for the survival and virulence of several human pathogens including Mycobacterium tuberculosis 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.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 201.57 kDa 
• Atom Count: 12,995 
• Modelled Residue Count: 1,717 
• Deposited Residue Count: 1,860 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial extracellular solute-binding protein	A [auth E]	465	Mycolicibacterium smegmatis MC2 155	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC sugar transporter, permease component	B [auth A]	305	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: sugA, MSMEI_4933, MSMEG_5060 Membrane Entity: Yes
UniProt
Find proteins for A0R2C2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R2C2  Go to UniProtKB:  A0R2C2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, permease protein SugB	C [auth B]	278	Mycolicibacterium smegmatis MC2 155	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, ATP-binding protein SugC	D [auth C], E [auth D]	406	Mycolicibacterium smegmatis MC2 155	Mutation(s): 1  Gene Names: MSMEG_5058
UniProt
Find proteins for A0R2C0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R2C0  Go to UniProtKB:  A0R2C0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	F [auth H]	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	H [auth C], J [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	G [auth C], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	F [auth H]	trehalose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Liu, F., Liang, J., Zhang, B., Gao, Y., Yang, X., Hu, T.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFC0840300
National Natural Science Foundation of China (NSFC)	China	81520108019

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release