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- PDB-8hpm: LpqY-SugABC in state 2 -

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Basic information

Entry
Database: PDB / ID: 8hpm
TitleLpqY-SugABC in state 2
Components
  • (ABC transporter, ...) x 2
  • ABC sugar transporter, permease component
  • Bacterial extracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Trehalose / ABC transporter / tuberculosis
Function / homology
Function and homology information


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
: / 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. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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. / Prokaryotic membrane lipoprotein lipid attachment site profile. / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Trehalose import ATP-binding protein SugC / ABC transporter, permease protein SugB / Bacterial extracellular solute-binding protein / ABC sugar transporter, permease component
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsLiang, J. / Yang, X. / Zhang, B. / Rao, Z. / Liu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200983 China
CitationJournal: Structure / Year: 2023
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.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
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Revision 1.1Oct 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC sugar transporter, permease component
B: ABC transporter, permease protein SugB
C: ABC transporter, ATP-binding protein SugC
D: ABC transporter, ATP-binding protein SugC
E: Bacterial extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,5248
Polymers200,1675
Non-polymers1,3573
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AE

#1: 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 MC2 155 (bacteria)
Gene: sugA, MSMEI_4933
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G6S2
#4: Protein Bacterial extracellular solute-binding protein / LpqY


Mass: 50183.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_5061
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R2C3

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ABC transporter, ... , 2 types, 3 molecules BCD

#2: 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 MC2 155 (bacteria)
Gene: MSMEG_5059
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R2C1
#3: Protein ABC transporter, ATP-binding protein SugC


Mass: 43702.625 Da / Num. of mol.: 2 / Mutation: E164N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_5058
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R2C0

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Sugars / Non-polymers , 2 types, 3 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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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: Trehalose-specific importer LpqY-SugABC complex / Type: COMPLEX / Entity ID: #4, #3, #1-#2 / 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 / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45938 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01213058
ELECTRON MICROSCOPYf_angle_d1.82217889
ELECTRON MICROSCOPYf_dihedral_angle_d19.4967789
ELECTRON MICROSCOPYf_chiral_restr0.0942161
ELECTRON MICROSCOPYf_plane_restr0.0122300

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