← Back to search
7lov

Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin

Method: X-RAY DIFFRACTION Dmax: 112.0 Å Quality: EXCELLENT
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Toxin B

Clostridioides difficile

UniProt P18177

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–545 Not recorded NOY (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 3 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；85 mM Sodium Citrate pH 5.6, 170 mM Ammonium Acetate, 25.5 % (w/v) PEG 4000, 15 %(v/v) Glycerol Resolution 2.50 Å R-free 0.248
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–545 Not recorded NOY (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 2 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；85 mM Sodium Citrate pH 5.6, 170 mM Ammonium Acetate, 25.5 % (w/v) PEG 4000, 15 %(v/v) Glycerol Resolution 2.50 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7LOV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BVL Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion Deposited 2005-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–542（542 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-543
Mutation：YES MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 1 TBR HEXATANTALUM DODECABROMIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 2.20 Å R-free 0.244
2BVM Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion Deposited 2005-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–541（541 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-541
Mutation：YES MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 2.55 Å R-free 0.245
4NC2 Crystal structure of TcdB-B1 bound to B39 VHH Deposited 2013-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2248–2366（119 aa） Fragment：UNP residues 2248-2366
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；295 K；0.86 M Sodium citrate, pH 6.7, 0.6 M TMAO, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.229
4NP4 Clostridium difficile toxin B CROP domain in complex with FAB domains of neutralizing antibody bezlotoxumab Deposited 2013-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1834–2099（266 aa） Fragment：CROP domain(UNP residues 1834-2099)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；4% PEG 4000, pH 7.5, VAPOR DIFFUSION, temperature 277K
Resolution 2.89 Å R-free 0.232
5UQM Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F Deposited 2017-02-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：residues 1-543
Not recorded MN MANGANESE (II) ION × 1 U2F URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；0.1 M MES, 0.2 ammonium sulfate, PEG 8k 16-34%
Resolution 2.03 Å R-free 0.228
5UQN Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F Deposited 2017-02-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：residues 1-543
Not recorded MN MANGANESE (II) ION × 1 U2F URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；0.1 M MES, 0.2 M ammonium sulfate, PEG 8k 16-34%
Resolution 2.06 Å R-free 0.234
5UQT Clostridium difficile Toxin B (TcdB) glucosyltransferase domain co-crystallized with apigenin Deposited 2017-02-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：residues 1-543
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 7.5-8.5, 0.2 M Mg(CH3CHOO)2, PEG 3350 5-25%
Resolution 2.75 Å R-free 0.236
5UQT Clostridium difficile Toxin B (TcdB) glucosyltransferase domain co-crystallized with apigenin Deposited 2017-02-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–543（543 aa） Fragment：residues 1-543
Not recorded MN MANGANESE (II) ION × 1 AGI 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 7.5-8.5, 0.2 M Mg(CH3CHOO)2, PEG 3350 5-25%
Resolution 2.75 Å R-free 0.236
6AR6 Clostridioides difficile toxinB with DLD-4 darpin Deposited 2017-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 4–1799（1796 aa）
Chain A 1834–2099（266 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
6OQ8 Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH 7F Deposited 2019-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–542（542 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Tris, pH 8.8, 0.4 M ammonium sulfate, and 24% PEG 3350
Resolution 2.20 Å R-free 0.220
6OQ8 Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH 7F Deposited 2019-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–542（542 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Tris, pH 8.8, 0.4 M ammonium sulfate, and 24% PEG 3350
Resolution 2.20 Å R-free 0.220
7LOU Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–543（542 aa）
Not recorded EDO 1,2-ETHANEDIOL × 9 UDP URIDINE-5'-DIPHOSPHATE × 1 IFM 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Ammonium phosphate monobasic, 20% w/v Polyethylene glycol 3,350
Resolution 1.82 Å R-free 0.252
7LOU Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–543（542 aa）
Not recorded EDO 1,2-ETHANEDIOL × 10 UDP URIDINE-5'-DIPHOSPHATE × 1 IFM 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Ammonium phosphate monobasic, 20% w/v Polyethylene glycol 3,350
Resolution 1.82 Å R-free 0.252
7ML7 Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection Deposited 2021-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1967（1967 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7N8X Partial C. difficile TcdB and CSPG4 fragment Deposited 2021-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 374–1876（1503 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7N95 state 1 of TcdB and FZD2 at pH5 Deposited 2021-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2366（2366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7N97 State 2 of TcdB and FZD2 at pH5 Deposited 2021-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–2366（2365 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7N9Q State 3 of TcdB and FZD2 at pH5 Deposited 2021-06-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–2366（2365 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7N9R state 4 of TcdB and FZD2 at pH5 Deposited 2021-06-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2366（2366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
7N9S TcdB and frizzled-2 CRD complex Deposited 2021-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–2366（2365 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7N9Y Full-length TcdB and CSPG4 (401-560) complex Deposited 2021-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–2366（2365 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7S0Y Structures of TcdB in complex with Cdc42 Deposited 2021-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–540（540 aa）
Not recorded MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 11 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate (pH 6.6), 2.4 M ammonium sulfate, and 2.5% (v/v) Jeffamine M-600 (pH 7.0)
Resolution 2.79 Å R-free 0.259
7SO5 Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 3–543（541 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M TRIS pH 8.2 and 39% polyethylene glycol 400
Resolution 1.80 Å R-free 0.223
7SO7 Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–538（538 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Na cacodylate, 0.2M CaCl2, 40% PEG400
Resolution 3.59 Å R-free 0.258
7SO7 Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B Deposited 2021-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–538（538 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Na cacodylate, 0.2M CaCl2, 40% PEG400
Resolution 3.59 Å R-free 0.258
8QEN cryo-EM structure of apo Clostridioides difficile toxin B Deposited 2023-09-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2366（2366 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；100 mM TRIS-HCl pH 7.5 200 mM NaCl 0.002% LMNG 0.0002% CHS 0.0002% GDN
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8QEO cryo-EM structure complex of Frizzled-7 and Clostridioides difficile toxin B Deposited 2023-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2366（2366 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；100 mM TRIS-HCl pH 7.5 200 mM NaCl 0.002% LMNG 0.0002% CHS 0.0002% GDN
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
8Y2L The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile Deposited 2024-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–543（542 aa）
Chain B 2–543（542 aa）
Chain C 2–543（542 aa）
Mutation：Y59C, E244G, S452A Mutation：Y59C, E244G, S452A Mutation：Y59C, E244G, S452A MN MANGANESE (II) ION × 3 UDP URIDINE-5'-DIPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01M RbCl, 0.01M SrAc2, 0.01M CsAc, 0.01M BaAc2, 0.1M BES, TEA pH7.5, 12.5% PEG4,000, 20% 1,2,6- Hexanetriol
Resolution 3.95 Å R-free 0.300
8Y9B TcdB1 in complex with mini-binder Deposited 2024-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–2366（2366 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BJA C. difficile Tcdb cysteine protease domain in complex with IP6 Deposited 2024-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 544–797（254 aa） Fragment：Cysteine protease domain
Chain B 544–797（254 aa） Fragment：Cysteine protease domain
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.1 M Tris HCl, pH 8.2, 36% (w/v) PEG2000 monomethyl ether
Resolution 2.10 Å R-free 0.257
9CM5 CryoEM Strucuture of TcdB in complex with De Novo Minibinder fzd48 Deposited 2024-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2100（2100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.61 Å
9MF4 De novo designed minibinder complexed with Clostridioides difficile Toxin B Deposited 2024-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2366（2366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；30s preblot incubation on grid. 2-3s blot time.
Resolution 3.02 Å
9NFU CryoEM Structure of De Novo Antibody Fragment scFv 6 with C. difficile Toxin B (TcdB) Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2100（2100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；150 mM NaCl, 40 mM Tris/ HCl pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9OHC CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with taurochenodeoxycholic acid (TCDCA) Deposited 2025-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2366（2366 aa）
Not recorded TUD TAUROCHENODEOXYCHOLIC ACID × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；500 micromolar of TCDCA was added before freezing.
cryo-EM vitrification conditions Cryogen ETHANE；30s preblot incubation on grid. 2-3s blot time.
Resolution 3.28 Å
9OHD CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with methyl cholate Deposited 2025-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2366（2366 aa）
Not recorded A1CBA methyl cholate × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；200 micromolar of methyl cholate was added before freezing.
cryo-EM vitrification conditions Cryogen ETHANE；30s preblot incubation on grid. 2-3s blot time.
Resolution 2.87 Å
9OHE CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the closed CROP state Deposited 2025-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2366（2366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；4% DMSO was added before freezing.
cryo-EM vitrification conditions Cryogen ETHANE；30s preblot incubation on grid. 2-3s blot time.
Resolution 3.59 Å
9OHF CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the open CROP state Deposited 2025-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2366（2366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；4% DMSO was added before freezing.
cryo-EM vitrification conditions Cryogen ETHANE；30s preblot incubation on grid. 2-3s blot time.
Resolution 3.19 Å

33 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCDB_CLODI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–546； UniProt 2–545 Author chain B； PDBConstruct 3–546； UniProt 2–545

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7lov

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7lov
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7lov
Deposition date deposition_date2021-02-10
Structure title titleCrystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin
Keywords keywordsinhibitors, TcdB, toxin, Kinetic isotope effects, KIEs, drug design, TRANSFERASE, TRANSFERASE-Inhibitor complex; TRANSFERASE/Inhibitor
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.56 Å
Radius of gyration Rg (electron density) rg_electron34.69 Å
Forward intensity I(0) i0249088000.00
Molecular weight molecular_weight126630.0 kDa
Excluded volume excluded_volume158080 ų
Envelope volume envelope_volume209310 ų
Hydration-shell volume shell_volume49601 ų
Envelope diameter envelope_diameter111.1 Å
Shell Rg shell_rg42.08 Å
Envelope Rg envelope_rg34.02 Å
Shape Rg shape_rg34.72 Å
Total Rg total_rg35.10 Å
Total atoms total_atoms8912
Residues n_residues1077
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.0 Å
Rg (real space) rg_real35.42 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real2.4910e+08
I(0) uncertainty (real space) i0_real_error3.7280e+06
Rg (reciprocal space) rg_reciprocal35.51 Å
I(0) (reciprocal space) i0_reciprocal249100000.0000
Solution quality estimate total_estimate0.9053
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.8 Å
Skewness Skewness skewness0.150
Kurtosis Kurtosis kurtosis-0.568
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30180000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.930
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▶

8. Citations (1)

▶

9. Files and Curves (10)