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- EMDB-30329: Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocat... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30329 | |||||||||
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Title | Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocation state | |||||||||
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![]() | ABC transporter / Lipoprotein / Trehalose / Trehalose-specific importer / Mycobacteria / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() : / 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Liu F / Liang J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 200.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
Images | ![]() | 49.1 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cafMC ![]() 7cadC ![]() 7caeC ![]() 7cagC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocat...
Entire | Name: Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocation state |
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Components |
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-Supramolecule #1: Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocat...
Supramolecule | Name: Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocation state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Bacterial extracellular solute-binding protein
Macromolecule | Name: Bacterial extracellular solute-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50.183086 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: ABC transporter, ATP-binding protein SugC
Macromolecule | Name: ABC transporter, ATP-binding protein SugC / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 43.702625 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: ABC sugar transporter, permease component
Macromolecule | Name: ABC sugar transporter, permease component / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 32.73925 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #4: ABC transporter, permease protein SugB
Macromolecule | Name: ABC transporter, permease protein SugB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.839441 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188042 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |