9ohd

CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with methyl cholate

Method: ELECTRON MICROSCOPY D_max: 195.7 Å Quality: GOOD

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

Toxin B

Clostridioides difficile

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 1–2366	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

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 9OHD	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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 method 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 method 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 method 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 method 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
7LOV Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin Deposited 2021-02-10	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 2–545（544 aa）	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
7LOV Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin Deposited 2021-02-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–545（544 aa）	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
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 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–2366（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 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 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 ligand/ion 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 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 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 method 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 method 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 method 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 method 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–2366（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 method 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 oligomeric state Different ligand/ion 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 method 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–2366（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 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 ligand/ion 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
9OHE CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the closed CROP state Deposited 2025-05-04	Different ligand/ion 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 ligand/ion 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 38 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 1–2366； UniProt 1–2366

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ohd
Deposition date deposition_date	2025-05-04
Structure title title	CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with methyl cholate
Keywords keywords	clostridioides difficile, Toxin B, TcdB, Bile acid, methyl cholate, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	61.56 Å
Radius of gyration Rg (electron density) rg_electron	62.14 Å
Forward intensity I(0) i0	996440000.00
Molecular weight molecular_weight	270780.0 kDa
Excluded volume excluded_volume	340840 Å³
Envelope volume envelope_volume	519960 Å³
Hydration-shell volume shell_volume	74900 Å³
Envelope diameter envelope_diameter	208.2 Å
Shell Rg shell_rg	54.61 Å
Envelope Rg envelope_rg	62.41 Å
Shape Rg shape_rg	61.78 Å
Total Rg total_rg	63.20 Å
Total atoms total_atoms	37632
Residues n_residues	2366
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	195.7 Å
Rg (real space) rg_real	62.45 Å
Rg uncertainty (real space) rg_real_error	1.90 Å
I(0) (real space) i0_real	9.9640e+08
I(0) uncertainty (real space) i0_real_error	2.2610e+07
Rg (reciprocal space) rg_reciprocal	60.75 Å
I(0) (reciprocal space) i0_reciprocal	993600000.0000
Solution quality estimate total_estimate	0.7892
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.0 Å
Skewness Skewness skewness	0.538
Kurtosis Kurtosis kurtosis	-0.544
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	57720000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.005

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Toxin B
Molecular weight formula_weight	270767.3 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	37632

MSLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDIYIDTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAINDTLESFRENLNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELIIDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDVRNFEEFKNGESFNLYEQELVERWNLAAASDILRISALKEIGGMYLDVDMLPGIQPDLFESIEKPSSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEEVQSSFESVLASKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVKQIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGSLGEDDNLDFSQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNLPELSTLLQEIRNNSNSSDIELEEKVMLTECEINVISNIDTQIVEERIEEAKNLTSDSINYIKDEFKLIESISDALCDLKQQNELEDSHFISFEDISETDEGFSIRFINKETGESIFVETEKTIFSEYANHITEEISKIKGTIFDTVNGKLVKKVNLDTTHEVNTLNAAFFIQSLIEYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAKVVELVSTALDETIDLLPTLSEGLPIIATIIDGVSLGAAIKELSETSDPLLRQEIEAKIGIMAVNLTTATTAIITSSLGIASGFSILLVPLAGISAGIPSLVNNELVLRDKATKVVDYFKHVSLVETEGVFTLLDDKIMMPQDDLVISEIDFNNNSIVLGKCEIWRMEGGSGHTVTDDIDHFFSAPSITYREPHLSIYDVLEVQKEELDLSKDLMVLPNAPNRVFAWETGWTPGLRSLENDGTKLLDRIRDNYEGEFYWRYFAFIADALITTLKPRYEDTNIRINLDSNTRSFIVPIITTEYIREKLSYSFYGSGGTYALSLSQYNMGINIELSESDVWIIDVDNVVRDVTIESDKIKKGDLIEGILSTLSIEENKIILNSHEINFSGEVNGSNGFVSLTFSILEGINAIIEVDLLSKSYKLLISGELKILMLNSNHIQQKIDYIGFNSELQKNIPYSFVDSEGKENGFINGSTKEGLFVSELPDVVLISKVYMDDSKPSFGYYSNNLKDVKVITKDNVNILTGYYLKDDIKISLSLTLQDEKTIKLNSVHLDESGVAEILKFMNRKGNTNTSDSLMSFLESMNIKSIFVNFLQSNIKFILDANFIISGTTSIGQFEFICDENDNIQPYFIKFNTLETNYTLYVGNRQNMIVEPNYDLDDSGDISSTVINFSQKYLYGIDSCVNKVVISPNIYTDEINITPVYETNNTYPEVIVLDANYINEKINVNINDLSIRYVWSNDGNDFILMSTSEENKVSQVKIRFVNVFKDKTLANKLSFNFSDKQDVPVSEIILSFTPSYYEDGLIGYDLGLVSLYNEKFYINNFGMMVSGLIYINDSLYYFKPPVNNLITGFVTVGDDKYYFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFKYFAPANTLDENLEGEAIDFTGKLIIDENIYYFDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLGNEEGEEISYSGILNFNNKIYYFDDSFTAVVGWKDLEDGSKYYFDEDTAEAYIGLSLINDGQYYFNDDGIMQVGFVTINDKVFYFSDSGIIESGVQNIDDNYFYIDDNGIVQIGVFDTSDGYKYFAPANTVNDNIYGQAVEYSGLVRVGEDVYYFGETYTIETGWIYDMENESDKYYFNPETKKACKGINLIDDIKYYFDEKGIMRTGLISFENNNYYFNENGEMQFGYINIEDKMFYFGEDGVMQIGVFNTPDGFKYFAHQNTLDENFEGESINYTGWLDLDEKRYYFTDEYIAATGSVIIDGEEYYFDPDTAQLVISEHHHHHH

来源 Source

来源生物 organism	Clostridioides difficile
NCBI Class编号 ncbi_taxonomy_id	1496
宿主生物 host_organism	Priestia megaterium

Entity 2 Entity 2 non-polymer

Description description	methyl cholate
Molecular weight formula_weight	422.6 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.87 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	339310

fit	/app/data/saxs_computation/oh/9ohd/9ohd.fit
pddf	/app/data/pr_computation/oh/9ohd/9ohd.pr.out
profile	/app/data/saxs_computation/oh/9ohd/9ohd.dat