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- PDB-10oi: Structure of Clostridium difficile Toxin B (TcdB) glucosyltransfe... -

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Basic information

Entry
Database: PDB / ID: 10oi
TitleStructure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP linked isofagomine analog 3-5
ComponentsToxin B
KeywordsTRANSFERASE / Inhibitor / Complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding
Similarity search - Function
TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain ...TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / : / URIDINE-5'-DIPHOSPHATE / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPaparella, A.S. / Gilaj, N. / Wagner, A.G. / Schramm, V.L. / Ghosh, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041916 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150971 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD020068 United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Isofagomine Derivatives as TcdB Glucosyltransferase Inhibitors.
Authors: Shaffer, K.J. / Gilaj, N. / Wagner, A.G. / Popadynec, M. / Groom, D.P. / Hughes, L.A. / Ghosh, A. / Paparella, A. / Tyler, P.C. / Lamiable-Oulaidi, F. / Schramm, V.L.
History
DepositionJan 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin B
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,68511
Polymers128,6282
Non-polymers2,0579
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.051, 82.568, 113.082
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Toxin B


Mass: 64313.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Amino acid residues 2-543 / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Non-polymers , 5 types, 108 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-A1C96 / 1-(5-O-{3-[(3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-1-yl]propyl}-alpha-L-lyxofuranosyl)pyrimidine-2,4(1H,3H)-dione


Mass: 431.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H29N3O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.085 M Tri-sodium citrate, 0.17 M Ammonium acetate, 25.5% (w/v) Polyethylene glycol 3,350 and 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 40877 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.9 Å2 / CC1/2: 0.97 / CC star: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.1 / Net I/σ(I): 6.8
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.9 / Num. unique obs: 2553 / CC1/2: 0.7 / CC star: 0.9 / Rpim(I) all: 0.35 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→24.95 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 2053 5.04 %
Rwork0.2214 --
obs0.2232 40766 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8804 0 130 99 9033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029154
X-RAY DIFFRACTIONf_angle_d0.44812368
X-RAY DIFFRACTIONf_dihedral_angle_d17.5673436
X-RAY DIFFRACTIONf_chiral_restr0.0371353
X-RAY DIFFRACTIONf_plane_restr0.0031587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.39421590.30812520X-RAY DIFFRACTION99
2.71-2.780.32431690.27632518X-RAY DIFFRACTION100
2.78-2.850.33881480.26282598X-RAY DIFFRACTION100
2.85-2.940.28071250.25532532X-RAY DIFFRACTION100
2.94-3.030.2963970.25532635X-RAY DIFFRACTION100
3.03-3.140.32241320.262561X-RAY DIFFRACTION100
3.14-3.270.28781140.24052589X-RAY DIFFRACTION100
3.27-3.410.28821470.24372576X-RAY DIFFRACTION100
3.41-3.590.24831220.22212595X-RAY DIFFRACTION100
3.59-3.820.26811380.20622568X-RAY DIFFRACTION100
3.82-4.110.20491220.18932619X-RAY DIFFRACTION100
4.11-4.520.22621470.18982569X-RAY DIFFRACTION100
4.52-5.170.21021750.19522561X-RAY DIFFRACTION100
5.17-6.50.28821410.23292580X-RAY DIFFRACTION100
6.5-24.950.17441170.18052692X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02630.04350.44410.5641-0.2871.5851-0.07930.3973-0.108-0.06250.10070.2039-0.0275-0.438-0.04070.2070.012-0.00570.5178-0.04470.2615.508216.194229.3858
22.3646-0.879-0.48294.3741-0.48062.48440.04580.0560.2705-0.153-0.059-0.7888-0.20150.31660.0010.1993-0.0060.05270.26720.03670.343958.763922.307345.0147
31.3276-1.2517-1.01881.71940.56811.43670.00920.06320.0477-0.1109-0.1065-0.02120.0346-0.03070.12230.1779-0.0532-0.0260.1758-0.01430.184634.354814.490250.8331
41.19180.0068-0.29270.59550.25071.19290.01960.21570.192-0.08860.0027-0.0127-0.1741-0.1356-0.02490.28690.0181-0.02190.17470.02530.249532.861424.432144.3059
53.30751.3654-2.62240.5305-0.99042.4393-0.2060.0127-0.25110.00890.05920.11520.1375-0.26640.13460.31260.01470.13920.3872-0.03130.47477.179653.455928.333
60.64670.7332-0.23851.44580.7821.87580.15140.0986-0.45550.05850.068-0.33270.01990.2835-0.13190.3198-0.0237-0.02270.1967-0.07170.395848.112654.12486.0809
70.73390.65580.30611.80480.53551.00670.080.0401-0.00180.1591-0.0828-0.12620.02360.1005-0.03230.28390.02710.0220.2468-0.00290.219343.126358.23949.8544
81.16710.37410.20331.51630.58661.73130.1693-0.0466-0.04080.0917-0.09190.11360.2511-0.3056-0.0270.29620.00290.02230.14870.05290.250531.800652.03888.6217
92.54850.38370.69291.06470.5561.87270.2533-0.3296-0.52660.3072-0.15120.22870.5815-0.2955-0.14130.4704-0.0650.03010.19420.01040.404328.670646.862819.4937
101.9288-3.04120.8214.8434-1.6092.41890.26270.4243-0.43220.17170.0467-0.27830.36580.5935-0.27680.34940.0747-0.04580.3665-0.20810.505250.182242.6163.0989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 323 )
4X-RAY DIFFRACTION4chain 'A' and (resid 324 through 539 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 168 through 323 )
8X-RAY DIFFRACTION8chain 'B' and (resid 324 through 437 )
9X-RAY DIFFRACTION9chain 'B' and (resid 438 through 511 )
10X-RAY DIFFRACTION10chain 'B' and (resid 512 through 540 )

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