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- EMDB-39493: Cryo-EM structure of BfUbb-ButCD complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39493
TitleCryo-EM structure of BfUbb-ButCD complex
Map data
Sample
  • Complex: ButCD-BfUbb complex
    • Protein or peptide: Membrane protein
    • Protein or peptide: TonB-linked outer membrane protein
    • Protein or peptide: Ubiquitin-like protein
Keywordstransporter / TonB-dependent / MEMBRANE PROTEIN
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Membrane protein / : / :
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsXu JH / Chen Z / Gao X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues.
Authors: Ming Tong / Jinghua Xu / Weixun Li / Kun Jiang / Yan Yang / Zhe Chen / Xuyao Jiao / Xiangfeng Meng / Mingyu Wang / Jie Hong / Hongan Long / Shuang-Jiang Liu / Bentley Lim / Xiang Gao /
Abstract: Efficient interbacterial competitions and diverse defensive strategies employed by various bacteria play a crucial role in acquiring a hold within a dense microbial community. The gut symbiont ...Efficient interbacterial competitions and diverse defensive strategies employed by various bacteria play a crucial role in acquiring a hold within a dense microbial community. The gut symbiont Bacteroides fragilis secretes an antimicrobial ubiquitin homologue (BfUbb) that targets an essential periplasmic PPIase to drive intraspecies bacterial competition. However, the mechanisms by which BfUbb enters the periplasm and its potential for interspecies antagonism remain poorly understood. Here, we employ transposon mutagenesis and identify a highly conserved TonB-dependent transporter SusCD (designated as ButCD) in B. fragilis as the BfUbb transporter. As a putative protein-related nutrient utilization system, ButCD is widely distributed across diverse Bacteroides species with varying sequence similarity, resulting in distinct import efficiency of Bacteroides ubiquitin homologues (BUbb) and thereby determining the species-specific toxicity of BUbb. Cryo-EM structural and functional investigations of the BfUbb-ButCD complex uncover distinctive structural features of ButC that are crucial for its targeting by BfUbb. Animal studies further demonstrate the specific and efficient elimination of enterotoxigenic B. fragilis (ETBF) in the murine gut by BfUbb, suggesting its potential as a therapeutic against ETBF-associated inflammatory bowel disease and colorectal cancer. Our findings provide a comprehensive elucidation of the species-specific toxicity exhibited by BUbb and explore its potential applications.
History
DepositionMar 18, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39493.png

Downloads & links

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Map

FileDownload / File: emd_39493.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 300 pix.
= 354. Å		1.18 Å/pix.
x 300 pix.
= 354. Å		1.18 Å/pix.
x 300 pix.
= 354. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-8.534674000000001 - 12.005243999999999
Average (Standard dev.)0.00058856944 (±0.282839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 353.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ButCD-BfUbb complex

EntireName: ButCD-BfUbb complex
Components
  • Complex: ButCD-BfUbb complex
    • Protein or peptide: Membrane protein
    • Protein or peptide: TonB-linked outer membrane protein
    • Protein or peptide: Ubiquitin-like protein

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Supramolecule #1: ButCD-BfUbb complex

SupramoleculeName: ButCD-BfUbb complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroides fragilis (bacteria)

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Macromolecule #1: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 48.007312 KDa
SequenceString: CDSYLDIRPV GSVIPQTAEE YRALLARAYL NVPNDRGLAC LRSDEMLVND NEYDRNSYGD IERWNDVSPF PGTSQFTWSN FYNVLFIAN QVIESQKEIT EGTPEVVNQL VGEAHLLRAY LHFVLVNLHG QPYTKSGALN SKSIPLKLDT DLEKTLGRNT V EEVYTSIL ...String:
CDSYLDIRPV GSVIPQTAEE YRALLARAYL NVPNDRGLAC LRSDEMLVND NEYDRNSYGD IERWNDVSPF PGTSQFTWSN FYNVLFIAN QVIESQKEIT EGTPEVVNQL VGEAHLLRAY LHFVLVNLHG QPYTKSGALN SKSIPLKLDT DLEKTLGRNT V EEVYTSIL SDIEHARELI NKEKWETVFS YRFNVLSVDA LQSRVSLYMG AWPKCLESAE AVLAKKSVLV DMNETPLALP NH FESVESI TALEQVMGSS VNNAVWVPAT FLALYQEGDK RLAAYFAAPD ENGNRKSSKG GKREFSCTFR VGELYLNAAE AAA NMDKLP HARMRLLELM RKRYTPEAYA KKENAVNVMD KNALISEILN ERARELAFEG HRWFDLRRTT RPRMVKVLQG KTYI LEQDD PRYTIPIPRD AIAANPGL

UniProtKB: Membrane protein

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Macromolecule #2: TonB-linked outer membrane protein

MacromoleculeName: TonB-linked outer membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 111.167352 KDa
SequenceString: DAVVVTGYQT VERRKLTAAV GKLNISDETI GAVKSIDQAL AGQIAGLSVT STSGAPGAPA KIRIRGTSSL NGTQDPLWVL DGIPLEGTD VPQSNVLNDV SNIQQSSIAG LNPADIENIT VLKDAAATAI YGARAANGVI VITTKKGKVG KPVINFSSKF T YMPTLSTN ...String:
DAVVVTGYQT VERRKLTAAV GKLNISDETI GAVKSIDQAL AGQIAGLSVT STSGAPGAPA KIRIRGTSSL NGTQDPLWVL DGIPLEGTD VPQSNVLNDV SNIQQSSIAG LNPADIENIT VLKDAAATAI YGARAANGVI VITTKKGKVG KPVINFSSKF T YMPTLSTN RLNMLNSQEK VDLELELLRS NFAYGDNKGG VSKIISGYGL TDAYKKGGWS ALTPEAQTDI SRLRNTETDW GD ILFRDAF NQEYSLSLSG GNERVTYYTS IGYYQENGNV KGVGLDRLNI VAKTSYKVNR MLKFGVSLFV NRRNNKTYLT DTY GLVNPV YYSRKANPYY QPFDANGNYV YDFDVQNNSD TDLGFNIFEE RKNTSNEETI NALSSIFDAE LRFNDKLKFT TQLG LQLDK ASKEQIADKE SFSMRIIRKN SKYWDSASQS NKYFIPDGGV HKAYENTNSQ ITWKAMGEYR DSFNDIHELE VMVGT ELRK TWYETLFSAG YGFDRQTLTT KPVVFPDEDR ARQFPLHQKT YKENAYVSFF STASYSLMNR YTFGGSIRFD GSDLFG VDK KYRYLPLYSV SGLWRLSNEP FMQGTRKWMD NLAFRVSYGI QGNIDKNTSP FLLGKYIVDN ILPGGSEHMI DINSAPN KK LRWEKTQSVN VGLDFSVLNQ ALNLSVDYYY RKGTDLIGKQ MLPLETGFVS TNINWASMVN KGVEVSLSTR NVATKNFS W YTNLNFAYNN NKVLREAIPE AQTIPGREGY PVDAIFAIKT AGLDEEGYPL FYDKEGKKVT LKELYRLQDP FGLGFTVNS DVTPAEERSF YSYIGSQDTP YTGGLINTFS YKNWELTANL SFNLGGYVRT TPSYNFINFD RGQNVNSDIL DRWTPENTDG RLPALITSE KRADEYYWYD QKSEIYKNLD IWVKKLNYFR LQNLRLGYRL PEKMTKSLGM GSASVAIEGR NLLVFGSSYK N FLDPESMY NPYAPPIPKS ITFSLNLN

UniProtKB: UNIPROTKB: A0A3E5IFP1

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Macromolecule #3: Ubiquitin-like protein

MacromoleculeName: Ubiquitin-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 8.79105 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQVFIKNRYG WTITLEVSPT DTVENVKQKI QDKEGFPPDK IRLIYGGKQM EDGRTLADYN VQKDSTILIC IRDVDC

UniProtKB: UNIPROTKB: A0A9Q4J272

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 298613
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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