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Yorodumi- EMDB-36125: Cryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36125 | |||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in complex with trehalose | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information ABC-type carbohydrate transporter activity / ATP-binding cassette (ABC) transporter complex, transmembrane substrate-binding subunit-containing / trehalose transmembrane transporter activity / trehalose transport / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space ...ABC-type carbohydrate transporter activity / ATP-binding cassette (ABC) transporter complex, transmembrane substrate-binding subunit-containing / trehalose transmembrane transporter activity / trehalose transport / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
Authors | Zhang B / Liang J / Rao Z | |||||||||
Funding support | China, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Molecular recognition of trehalose and trehalose analogues by LpqY-SugABC. Authors: Jingxi Liang / Fengjiang Liu / Peng Xu / Wei Shangguan / Tianyu Hu / Shule Wang / Xiaolin Yang / Zhiqi Xiong / Xiuna Yang / Luke W Guddat / Biao Yu / Zihe Rao / Bing Zhang / Abstract: Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen (). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter ...Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen (). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter . The substrate-binding protein, LpqY, which forms a stable complex with the translocator SugABC, recognizes and captures trehalose and its analogues in the periplasmic space, but the precise molecular mechanism for this process is still not well understood. This study reports a 3.02-Å cryoelectron microscopy structure of trehalose-bound LpqY-SugABC in the pretranslocation state, a crystal structure of LpqY in a closed form with trehalose bound and five crystal structures of LpqY in complex with different trehalose analogues. These structures, accompanied by substrate-stimulated ATPase activity data, reveal how LpqY recognizes and binds trehalose and its analogues, and highlight the flexibility in the substrate binding pocket of LpqY. These data provide critical insights into the design of trehalose analogues that could serve as potential molecular probe tools or as anti-TB drugs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36125.map.gz | 107.9 MB | EMDB map data format | |
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Header (meta data) | emd-36125-v30.xml emd-36125.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_36125.png | 35.6 KB | ||
Filedesc metadata | emd-36125.cif.gz | 6.3 KB | ||
Others | emd_36125_half_map_1.map.gz emd_36125_half_map_2.map.gz | 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36125 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36125 | HTTPS FTP |
-Validation report
Summary document | emd_36125_validation.pdf.gz | 940.2 KB | Display | EMDB validaton report |
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Full document | emd_36125_full_validation.pdf.gz | 939.7 KB | Display | |
Data in XML | emd_36125_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_36125_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36125 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36125 | HTTPS FTP |
-Related structure data
Related structure data | 8ja7MC 8ja8C 8ja9C 8jaaC 8jabC 8jacC 8jadC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36125.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36125_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36125_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : LpqY-SugABC
Entire | Name: LpqY-SugABC |
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Components |
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-Supramolecule #1: LpqY-SugABC
Supramolecule | Name: LpqY-SugABC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
-Macromolecule #1: Trehalose transport system permease protein SugA
Macromolecule | Name: Trehalose transport system permease protein SugA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 33.041809 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: VTSVEQRTAT AVFSRTGSRM AERRLAFMLV APAAMLMVAV TAYPIGYALW LSLQRNNLAT PNDTAFIGLG NYHTILIDRY WWTALAVTL AITAVSVTIE FVLGLALALV MHRTLIGKGL VRTAVLIPYG IVTVVASYSW YYAWTPGTGY LANLLPYDSA P LTQQIPSL ...String: VTSVEQRTAT AVFSRTGSRM AERRLAFMLV APAAMLMVAV TAYPIGYALW LSLQRNNLAT PNDTAFIGLG NYHTILIDRY WWTALAVTL AITAVSVTIE FVLGLALALV MHRTLIGKGL VRTAVLIPYG IVTVVASYSW YYAWTPGTGY LANLLPYDSA P LTQQIPSL GIVVIAEVWK TTPFMSLLLL AGLALVPEDL LRAAQVDGAS AWRRLTKVIL PMIKPAIVVA LLFRTLDAFR IF DNIYVLT GGSNNTGSVS ILGYDNLFKG FNVGLGSAIS VLIFGCVAVI AFIFIKLFGA AAPGGEPSGR UniProtKB: Trehalose transport system permease protein SugA |
-Macromolecule #2: Trehalose transport system permease protein SugB
Macromolecule | Name: Trehalose transport system permease protein SugB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 29.145537 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: VGARRATYWA VLDTLVVGYA LLPVLWIFSL SLKPTSTVKD GKLIPSTVTF DNYRGIFRGD LFSSALINSI GIGLITTVIA VVLGAMAAY AVARLEFPGK RLLIGAALLI TMFPSISLVT PLFNIERAIG LFDTWPGLIL PYITFALPLA IYTLSAFFRE I PWDLEKAA ...String: VGARRATYWA VLDTLVVGYA LLPVLWIFSL SLKPTSTVKD GKLIPSTVTF DNYRGIFRGD LFSSALINSI GIGLITTVIA VVLGAMAAY AVARLEFPGK RLLIGAALLI TMFPSISLVT PLFNIERAIG LFDTWPGLIL PYITFALPLA IYTLSAFFRE I PWDLEKAA KMDGATPGQA FRKVIVPLAA PGLVTAAILV FIFAWNDLLL ALSLTATKAA ITAPVAIANF TGSSQFEEPT GS IAAGAIV ITIPIIVFVL IFQRRIVAGL TSGAVKG UniProtKB: Trehalose transport system permease protein SugB |
-Macromolecule #3: Trehalose-binding lipoprotein LpqY
Macromolecule | Name: Trehalose-binding lipoprotein LpqY / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 49.803074 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: VVMSRGRIPR LGAAVLVALT TAAAACGADS QGLVVSFYTP ATDGATFTAI AQRCNQQFGG RFTIAQVSLP RSPNEQRLQL ARRLTGNDR TLDVMALDVV WTAEFAEAGW ALPLSDDPAG LAENDAVADT LPGPLATAGW NHKLYAAPVT TNTQLLWYRP D LVNSPPTD ...String: VVMSRGRIPR LGAAVLVALT TAAAACGADS QGLVVSFYTP ATDGATFTAI AQRCNQQFGG RFTIAQVSLP RSPNEQRLQL ARRLTGNDR TLDVMALDVV WTAEFAEAGW ALPLSDDPAG LAENDAVADT LPGPLATAGW NHKLYAAPVT TNTQLLWYRP D LVNSPPTD WNAMIAEAAR LHAAGEPSWI AVQANQGEGL VVWFNTLLVS AGGSVLSEDG RHVTLTDTPA HRAATVSALQ IL KSVATTP GADPSITRTE EGSARLAFEQ GKAALEVNWP FVFASMLENA VKGGVPFLPL NRIPQLAGSI NDIGTFTPSD EQF RIAYDA SQQVFGFAPY PAVAPGQPAK VTIGGLNLAV AKTTRHRAEA FEAVRCLRDQ HNQRYVSLEG GLPAVRASLY SDPQ FQAKY PMHAIIRQQL TDAAVRPATP VYQALSIRLA AVLSPITEID PESTADELAA QAQKAIDGMG LLP UniProtKB: Trehalose-binding lipoprotein LpqY |
-Macromolecule #4: Trehalose import ATP-binding protein SugC
Macromolecule | Name: Trehalose import ATP-binding protein SugC / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 42.964078 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MAEIVLDHVN KSYPDGHTAV RDLNLTIADG EFLILVGPSG CGKTTTLNMI AGLEDISSGE LRIAGERVNE KAPKDRDIAM VFQSYALYP HMTVRQNIAF PLTLAKMRKA DIAQKVSETA KILDLTNLLD RKPSQLSGGQ RQRVAMGRAI VRHPKAFLMD E PLSNLDAK ...String: MAEIVLDHVN KSYPDGHTAV RDLNLTIADG EFLILVGPSG CGKTTTLNMI AGLEDISSGE LRIAGERVNE KAPKDRDIAM VFQSYALYP HMTVRQNIAF PLTLAKMRKA DIAQKVSETA KILDLTNLLD RKPSQLSGGQ RQRVAMGRAI VRHPKAFLMD E PLSNLDAK LRVQMRGEIA QLQRRLGTTT VYVTHDQTEA MTLGDRVVVM YGGIAQQIGT PEELYERPAN LFVAGFIGSP AM NFFPARL TAIGLTLPFG EVTLAPEVQG VIAAHPKPEN VIVGVRPEHI QDAALIDAYQ RIRALTFQVK VNLVESLGAD KYL YFTTES PAVHSVQLDE LAEVEGESAL HENQFVARVP AESKVAIGQS VELAFDTARL AVFDADSGAN LTIPHRA UniProtKB: Trehalose import ATP-binding protein SugC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50775 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |