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- EMDB-60115: Cryo-EM map of PpiD-YfgM-Bte1 complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-60115
TitleCryo-EM map of PpiD-YfgM-Bte1 complex
Map data
Sample
  • Complex: complex of PpiD-YfgM-Bte1
    • Protein or peptide: PpiD
    • Protein or peptide: YfgM
    • Protein or peptide: Bte1
Keywordscomplex / ISOMERASE
Biological speciesBacteroides (bacteria) / Bacteroides thetaiotaomicron (bacteria) / Bacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXu JH / Chen Z / Gao X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2025
Title: A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.
Authors: Bentley Lim / Jinghua Xu / Igor H Wierzbicki / Carlos G Gonzalez / Zhe Chen / David J Gonzalez / Xiang Gao / Andrew L Goodman /
Abstract: Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, ...Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.
History
DepositionMay 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60115.png

Downloads & links

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Map

FileDownload / File: emd_60115.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 220 pix.
= 224.4 Å		1.02 Å/pix.
x 220 pix.
= 224.4 Å		1.02 Å/pix.
x 220 pix.
= 224.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.4155216 - 3.0530672
Average (Standard dev.)-0.0005057843 (±0.06065011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 224.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60115_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60115_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 : complex of PpiD-YfgM-Bte1

EntireName: complex of PpiD-YfgM-Bte1
Components
  • Complex: complex of PpiD-YfgM-Bte1
    • Protein or peptide: PpiD
    • Protein or peptide: YfgM
    • Protein or peptide: Bte1

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Supramolecule #1: complex of PpiD-YfgM-Bte1

SupramoleculeName: complex of PpiD-YfgM-Bte1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroides (bacteria)

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Macromolecule #1: PpiD

MacromoleculeName: PpiD / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQPHQAHDVG EVNGDALSAQ EYQNLVEEYT EVIKLSRGVT ALNDEQTNQV RDEVWRSYVN NKLVEKEAKA LGLTVSAAEI QDILKAGVHP LLQQTPFRNP QTGAFDKDML NKFLVDYAKM NESQMPAQYA EQYNNMYKYW SFIQKTLVQS RLAEKYQALV AKALLSNPVE ...String:
MQPHQAHDVG EVNGDALSAQ EYQNLVEEYT EVIKLSRGVT ALNDEQTNQV RDEVWRSYVN NKLVEKEAKA LGLTVSAAEI QDILKAGVHP LLQQTPFRNP QTGAFDKDML NKFLVDYAKM NESQMPAQYA EQYNNMYKYW SFIQKTLVQS RLAEKYQALV AKALLSNPVE AQDAFDARVN QYDLLMAAVP YSSIVDSTIV VKESELKDLY NKKKEQFKQY QESRDIKYID VQVTASAEDR AAIQQEVDEA TAQLATTTDD YTSFIRSVGS EAPYVDLFYN KTAFPSDVVA RLDSASVGSV YGPYYNGADN TINSFKVVAK TAAADSIEFR QIQVFAEDAL KTKALADSIY TAIKGGANFA DLAKKYGQTG ETNWMSSAQY EGAQIDGDNL KFISAINNTG VNEVVNLPLG QANVILQVTN KKAVKDKYKV AVVKREVEFS KETYNRAYND FSQFIAANPT AEKMIANAEE AGYKLLDRRD LYSSEHTIGG VRGTKEALRW AFSAKPGDVS GLYECGESDH MVAVALVGVT PEGYRPLKAV QDQLRAEIVK DKKAEKIMAD MKAANATSLD QYKAMSGAVS DSLKLVTFAA PAYVSALRSS EPLVGAYASV AEMNKLSAPI KGNAGVFVLQ MYGKDKLSDT FNAKDEEATL ANMHARFASR LMNDLYLKGK VKDTRYLFFL EHHHHHH

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Macromolecule #2: YfgM

MacromoleculeName: YfgM / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
EEKAQAALFK GQEYFEQDAY EQALNGDSIG YVGFLKVADE YSGTKAANLA KAYAGICYAQ LGKYDEAVKM LDGFNGGDQM VAPAILGATG NCYAQLGQLD KAASTLLSAA DKADNNSLSP IFLMQAGEIL VKQGKYDDAV NAYTKIKDKY FQSYQAMDID KYIEQAKLMK K

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Macromolecule #3: Bte1

MacromoleculeName: Bte1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GKEIEIKKLP EFEAMVNAGN TTYTGLVEGI GYVYWTTETL YFIRTNPEQL WAIPKYQQIP FPYFQRKDAI IETKTLHTLH VLSKDELLKL DYDAYYAFYG IVEEMLKFIH RADAIKSYCE IPLPIIKSKG ALKGNDARNG ILSLGSQIND QIGAPLDAAN MLMDNKHIGK ...String:
GKEIEIKKLP EFEAMVNAGN TTYTGLVEGI GYVYWTTETL YFIRTNPEQL WAIPKYQQIP FPYFQRKDAI IETKTLHTLH VLSKDELLKL DYDAYYAFYG IVEEMLKFIH RADAIKSYCE IPLPIIKSKG ALKGNDARNG ILSLGSQIND QIGAPLDAAN MLMDNKHIGK IGDGLSLISI IDEVGNGEYW SAAGDILLFA AGKTKLSPYM TVISLGTWMY ETDLMQWRLA CINYSDYKKT LIKYRELQKK FESGDKSVEE KMNECHKILN SHYIEMQKNL GNLGVKF

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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: GATAN K3 (6k 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: 2.5 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151004
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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