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- PDB-7cad: Mycobacterium smegmatis SugABC complex -

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Basic information

Entry
Database: PDB / ID: 7cad
TitleMycobacterium smegmatis SugABC complex
Components
  • ABC sugar transporter, permease component
  • ABC transporter, ATP-binding protein SugC
  • ABC transporter, permease protein SugB
KeywordsTRANSPORT PROTEIN / ABC transporter / Lipoprotein / Mycobacteria
Function / homology
Function and homology information


carbohydrate 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
: / MalK, OB fold domain / MetI-like fold / MetI-like / : / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like ...: / MalK, OB fold domain / MetI-like fold / MetI-like / : / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ABC transporter, ATP-binding protein SugC / ABC transporter, permease protein SugB / ABC transporter, permease protein SugA / ABC sugar transporter, permease component
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLiu, F. / Liang, J. / Zhang, B. / Gao, Y. / Yang, X. / Hu, T. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
National Natural Science Foundation of China (NSFC)81520108019 China
CitationJournal: Sci Adv / Year: 2020
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
DepositionJun 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
C: ABC transporter, ATP-binding protein SugC
D: ABC transporter, ATP-binding protein SugC
A: ABC sugar transporter, permease component
B: ABC transporter, permease protein SugB


Theoretical massNumber of molelcules
Total (without water)149,9864
Polymers149,9864
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ABC transporter, ATP-binding protein SugC


Mass: 43703.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5058
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R2C0
#2: Protein ABC sugar transporter, permease component / SugA


Mass: 32739.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: sugA, MSMEI_4933
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G6S2, UniProt: A0R2C2*PLUS
#3: Protein ABC transporter, permease protein SugB


Mass: 29839.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5059
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R2C1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycobacterium smegmatis SugABC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197191 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410219
ELECTRON MICROSCOPYf_angle_d0.63713911
ELECTRON MICROSCOPYf_dihedral_angle_d11.8066120
ELECTRON MICROSCOPYf_chiral_restr0.0461675
ELECTRON MICROSCOPYf_plane_restr0.0041764

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