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- PDB-8zht: Structure of PpiD-YfgM complex -

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Basic information

Entry
Database: PDB / ID: 8zht
TitleStructure of PpiD-YfgM complex
Components
  • Peptidyl-prolyl cis-trans isomerase
  • Tetratricopeptide repeat protein
KeywordsCHAPERONE / complex
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / membrane / plasma membrane
Similarity search - Function
Tetratricopeptide repeat-like domain / Tetratricopeptide repeat-like domain / SurA-like N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase / Tetratricopeptide repeat protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsXu, J.H. / Chen, Z. / Gao, X.
Funding support1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
B: Tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5703
Polymers93,4642
Non-polymers1061
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-26 kcal/mol
Surface area43130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.566, 81.347, 212.851
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / Peptidylprolyl isomerase


Mass: 74581.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BSIG_2281, ERS852557_00524, GAN91_18610, GAN93_09860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N7IAL9
#2: Protein Tetratricopeptide repeat protein / Tetratricopeptide repeat-containing protein


Mass: 18882.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BSIG_2392, Btheta7330_03850, DW780_14010, DWY18_22515, DXA83_21110, EH213_04903, ERS852557_00424, GAC70_07455, GAN59_22880, GAN75_05850, GAN91_20490, GAN93_09345, GAO00_04865, GAO51_05230, KQP59_08650, KQP68_01930
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0P0FRN2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Sodium citrate, n-Octyl-D-glucopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→34.19 Å / Num. obs: 65423 / % possible obs: 95.56 % / Redundancy: 9.9 % / Biso Wilson estimate: 42.86 Å2 / CC1/2: 0.98 / Net I/σ(I): 1.49
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 65423 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.19 Å / SU ML: 0.3215 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2181 822 3.05 %
Rwork0.1806 26127 -
obs0.1818 26949 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.25 Å2
Refinement stepCycle: LAST / Resolution: 3→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 7 377 6875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746604
X-RAY DIFFRACTIONf_angle_d0.84788918
X-RAY DIFFRACTIONf_chiral_restr0.0464989
X-RAY DIFFRACTIONf_plane_restr0.00591163
X-RAY DIFFRACTIONf_dihedral_angle_d17.77652433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.30551340.2224323X-RAY DIFFRACTION99.11
3.19-3.430.27141410.21264287X-RAY DIFFRACTION98.73
3.43-3.780.26351310.19724321X-RAY DIFFRACTION99.07
3.78-4.320.19971340.17054374X-RAY DIFFRACTION98.99
4.32-5.450.18731410.16744331X-RAY DIFFRACTION97.22
5.45-34.190.16731410.15484491X-RAY DIFFRACTION96.98

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