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- EMDB-30328: Mycobacterium smegmatis LpqY-SugABC complex in the resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-30328
TitleMycobacterium smegmatis LpqY-SugABC complex in the resting state
Map data
Sample
  • Complex: Mycobacterium smegmatis LpqY-SugABC complex in the resting state.
    • Protein or peptide: ABC transporter, ATP-binding protein SugCATP-binding cassette transporter
    • Protein or peptide: ABC sugar transporter, permease component
    • Protein or peptide: ABC transporter, permease protein SugBATP-binding cassette transporter
    • Protein or peptide: Bacterial extracellular solute-binding protein
KeywordsABC transporter / Lipoprotein / Mycobacteria / 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 / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein ...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 / ABC transporter, permease protein SugA / Bacterial extracellular solute-binding protein / ABC sugar transporter, permease component
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsLiu F / Liang J
Funding support China, 2 items
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, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cae
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30328.png

Downloads & links

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Map

FileDownload / File: emd_30328.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.6295914 - 0.84711134
Average (Standard dev.)0.00025420444 (±0.020934718)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.6300.8470.000

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Supplemental data

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Sample components

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Entire : Mycobacterium smegmatis LpqY-SugABC complex in the resting state.

EntireName: Mycobacterium smegmatis LpqY-SugABC complex in the resting state.
Components
  • Complex: Mycobacterium smegmatis LpqY-SugABC complex in the resting state.
    • Protein or peptide: ABC transporter, ATP-binding protein SugCATP-binding cassette transporter
    • Protein or peptide: ABC sugar transporter, permease component
    • Protein or peptide: ABC transporter, permease protein SugBATP-binding cassette transporter
    • Protein or peptide: Bacterial extracellular solute-binding protein

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Supramolecule #1: Mycobacterium smegmatis LpqY-SugABC complex in the resting state.

SupramoleculeName: Mycobacterium smegmatis LpqY-SugABC complex in the resting state.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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

MacromoleculeName: ABC transporter, ATP-binding protein SugC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
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 #2: ABC sugar transporter, permease component

MacromoleculeName: ABC sugar transporter, permease component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
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 #3: ABC transporter, permease protein SugB

MacromoleculeName: ABC transporter, permease protein SugB / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
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 #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 (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
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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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215265

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