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- EMDB-34932: LpqY-SugABC in state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-34932
TitleLpqY-SugABC in state 1
Map data
Sample
  • Complex: Trehalose-specific importer LpqY-SugABC complex
    • Protein or peptide: ABC transporter, ATP-binding protein SugC
    • Protein or peptide: ABC sugar transporter, permease component
    • Protein or peptide: ABC transporter, permease protein SugB
    • Protein or peptide: Bacterial extracellular solute-binding protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsTrehalose / ABC transporter / tuberculosis / TRANSPORT PROTEIN
Function / homology
Function and homology information


carbohydrate transport / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / MalK, OB fold domain / : / 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 ...: / MalK, OB fold domain / : / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter, 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.29 Å
AuthorsLiang J / Yang X / Zhang B / Rao Z / Liu F
Funding support China, 1 items
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, 2022-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34932.png

Downloads & links

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Map

FileDownload / File: emd_34932.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16675541 - 0.30001253
Average (Standard dev.)-0.00013459162 (±0.009400596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34932_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34932_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34932_half_map_2.map
Projections & Slices
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Sample components

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Entire : Trehalose-specific importer LpqY-SugABC complex

EntireName: Trehalose-specific importer LpqY-SugABC complex
Components
  • Complex: Trehalose-specific importer LpqY-SugABC complex
    • Protein or peptide: ABC transporter, ATP-binding protein SugC
    • Protein or peptide: ABC sugar transporter, permease component
    • Protein or peptide: ABC transporter, permease protein SugB
    • Protein or peptide: Bacterial extracellular solute-binding protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Trehalose-specific importer LpqY-SugABC complex

SupramoleculeName: Trehalose-specific importer LpqY-SugABC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2, #4
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: ABC sugar transporter, permease component

MacromoleculeName: ABC sugar transporter, permease component / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 32.73925 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTAAVTPSAS AVASDDKKSE RRLAFWLIAP AVLLMLAVTA YPIGYAVWLS LQRYNLAEPH DTEFIGLANY VTVLTDGYWW TAFAVTLGI TVVSVAIEFA LGLALALVMH RTIFGKGAVR TAILIPYGIV TVAASYSWYY AWTPGTGYLA NLLPEGSAPL T DQLPSLAI ...String:
MTAAVTPSAS AVASDDKKSE RRLAFWLIAP AVLLMLAVTA YPIGYAVWLS LQRYNLAEPH DTEFIGLANY VTVLTDGYWW TAFAVTLGI TVVSVAIEFA LGLALALVMH RTIFGKGAVR TAILIPYGIV TVAASYSWYY AWTPGTGYLA NLLPEGSAPL T DQLPSLAI VVLAEVWKTT PFMALLLLAG LALVPQDLLN AAQVDGAGPW KRLTKVILPM IKPAILVALL FRTLDAFRIF DN IYILTGG SNDTGSVSIL GYDNLFKAFN VGLGSAISVL IFLSVAIIAF IYIKIFGAAA PGSDEEVR

UniProtKB: ABC sugar transporter, permease component

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Macromolecule #2: ABC transporter, permease protein SugB

MacromoleculeName: ABC transporter, permease protein SugB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 29.839441 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MADRVDARRA TWWSVVNILV IVYALIPVLW ILSLSLKPTS SVKDGKLIPT EITFANYKAI FSGDAFTSAL FNSIGIGLIT TIIAVVIGG MAAYAVARLQ FPGKQLLIGV ALLIAMFPHI SLVTPIFNMW RGIGLFDTWP GLIIPYITFA LPLAIYTLSA F FREIPWDL ...String:
MADRVDARRA TWWSVVNILV IVYALIPVLW ILSLSLKPTS SVKDGKLIPT EITFANYKAI FSGDAFTSAL FNSIGIGLIT TIIAVVIGG MAAYAVARLQ FPGKQLLIGV ALLIAMFPHI SLVTPIFNMW RGIGLFDTWP GLIIPYITFA LPLAIYTLSA F FREIPWDL EKAAKMDGAT PAQAFRKVIA PLAAPGIVTA AILVFIFAWN DLLLALSLTA TQRAITAPVA IANFTGSSQF EE PTGSIAA GAMVITIPII IFVLIFQRRI VAGLTSGAVK G

UniProtKB: ABC transporter, permease protein SugB

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Macromolecule #3: ABC transporter, ATP-binding protein SugC

MacromoleculeName: ABC transporter, ATP-binding protein SugC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 43.702625 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MAEIVLDRVT KSYPDGAGGV RAAVKEFSMT IADGEFIILV GPSGCGKSTT LNMIAGLEEI TSGELRIGGE RVNEKAPKDR DIAMVFQSY ALYPHMTVRQ NIAFPLTLAK VPKAEIAAKV EETAKILDLS ELLDRKPGQL SGGQRQRVAM GRAIVRSPKA F LMDQPLSN ...String:
MAEIVLDRVT KSYPDGAGGV RAAVKEFSMT IADGEFIILV GPSGCGKSTT LNMIAGLEEI TSGELRIGGE RVNEKAPKDR DIAMVFQSY ALYPHMTVRQ NIAFPLTLAK VPKAEIAAKV EETAKILDLS ELLDRKPGQL SGGQRQRVAM GRAIVRSPKA F LMDQPLSN LDAKLRVQMR AEISRLQDRL GTTTVYVTHD QTEAMTLGDR VVVMLAGEVQ QIGTPDELYS SPANLFVAGF IG SPAMNFF PATRTDVGVR LPFGEVTLTP HMLDLLDKQA RPENIIVGIR PEHIEDSALL DGYARIRALT FSVRADIVES LGA DKYVHF TTEGAGAESA QLAELAADSG AGTNQFIARV SADSRVRTGE QIELAIDTTK LSIFDAATGL NLTRDITPTD PTEA AGPDA G

UniProtKB: ABC transporter, ATP-binding protein SugC

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Macromolecule #4: Bacterial extracellular solute-binding protein

MacromoleculeName: Bacterial extracellular solute-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 50.183086 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MRARRLCAAA VAAMAAASMV SACGSQTGGI VINYYTPANE EATFKAVANR CNEQLGGRFQ IAQRNLPKGA DDQRLQLARR LTGNDKSLD VMALDVVWTA EFAEAGWAVP LSEDPAGLAE ADATENTLPG PLETARWQDE LYAAPITTNT QLLWYRADLM P APPTTWDG ...String:
MRARRLCAAA VAAMAAASMV SACGSQTGGI VINYYTPANE EATFKAVANR CNEQLGGRFQ IAQRNLPKGA DDQRLQLARR LTGNDKSLD VMALDVVWTA EFAEAGWAVP LSEDPAGLAE ADATENTLPG PLETARWQDE LYAAPITTNT QLLWYRADLM P APPTTWDG MLDEANRLYR EGGPSWIAVQ GKQYEGMVVW FNTLLQSAGG QVLSDDGQRV TLTDTPEHRA ATVKALRIIK SV ATAPGAD PSITQTDENT ARLALEQGKA ALEVNWPYVL PSLLENAVKG GVSFLPLDGD PALQGSINDV GTFSPTDEQF DIA FDASKK VFGFAPYPGV NPDEPARVTL GGLNLAVAST SQHKAEAFEA IRCLRNVENQ RYTSIEGGLP AVRTSLYDDP AFQK KYPQY EIIRQQLTNA AVRPATPVYQ AVSTRMSATL APISDIDPER TADELTEAVQ KAIDGKGLIP

UniProtKB: Bacterial extracellular solute-binding protein

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49940
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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