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- EMDB-36125: Cryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-36125
TitleCryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in complex with trehalose
Map data
Sample
  • Complex: LpqY-SugABC
    • Protein or peptide: Trehalose transport system permease protein SugA
    • Protein or peptide: Trehalose transport system permease protein SugB
    • Protein or peptide: Trehalose-binding lipoprotein LpqY
    • Protein or peptide: Trehalose import ATP-binding protein SugC
KeywordsABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex, transmembrane substrate-binding subunit-containing / ABC-type carbohydrate transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport ...ATP-binding cassette (ABC) transporter complex, transmembrane substrate-binding subunit-containing / ABC-type carbohydrate transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / ATP hydrolysis activity / protein homodimerization activity / ATP binding / identical protein 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
Trehalose transport system permease protein SugB / Trehalose transport system permease protein SugA / Trehalose-binding lipoprotein LpqY / Trehalose import ATP-binding protein SugC
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZhang B / Liang J / Rao Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
National Natural Science Foundation of China (NSFC)32200983 China
CitationJournal: 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
DepositionMay 5, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36125.png

Downloads & links

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Map

FileDownload / File: emd_36125.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.151
Minimum - Maximum-0.50699776 - 1.1597403
Average (Standard dev.)-0.00035222954 (±0.032655872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36125_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36125_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LpqY-SugABC

EntireName: LpqY-SugABC
Components
  • Complex: LpqY-SugABC
    • Protein or peptide: Trehalose transport system permease protein SugA
    • Protein or peptide: Trehalose transport system permease protein SugB
    • Protein or peptide: Trehalose-binding lipoprotein LpqY
    • Protein or peptide: Trehalose import ATP-binding protein SugC

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Supramolecule #1: LpqY-SugABC

SupramoleculeName: LpqY-SugABC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

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Macromolecule #1: Trehalose transport system permease protein SugA

MacromoleculeName: Trehalose transport system permease protein SugA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 33.041809 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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Macromolecule #2: Trehalose transport system permease protein SugB

MacromoleculeName: Trehalose transport system permease protein SugB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 29.145537 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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Macromolecule #3: Trehalose-binding lipoprotein LpqY

MacromoleculeName: Trehalose-binding lipoprotein LpqY / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 49.803074 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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Macromolecule #4: Trehalose import ATP-binding protein SugC

MacromoleculeName: 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
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 42.964078 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: 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

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7caf

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50775

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