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- PDB-7uby: Structure of the GTD domain of Clostridium difficile toxin A in c... -

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Basic information

Entry
Database: PDB / ID: 7uby
TitleStructure of the GTD domain of Clostridium difficile toxin A in complex with VHH AH3
Components
  • Glucosyltransferase TcdA
  • Nanobody VHH AH3
KeywordsTOXIN / GTD / neutralizing antibody
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / glycosyltransferase activity / 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 ...Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / glycosyltransferase activity / 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 / membrane
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Toxin A
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, B. / Rongsheng, J. / Kay, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2022
Title: Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies.
Authors: Chen, B. / Perry, K. / Jin, R.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glucosyltransferase TcdA
D: Nanobody VHH AH3
A: Glucosyltransferase TcdA
C: Nanobody VHH AH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,20321
Polymers158,0664
Non-polymers2,13717
Water6,143341
1
B: Glucosyltransferase TcdA
D: Nanobody VHH AH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,11510
Polymers79,0332
Non-polymers1,0828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-10 kcal/mol
Surface area28500 Å2
MethodPISA
2
A: Glucosyltransferase TcdA
C: Nanobody VHH AH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,08911
Polymers79,0332
Non-polymers1,0569
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-7 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.118, 131.641, 83.796
Angle α, β, γ (deg.)90.000, 110.015, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Antibody , 2 types, 4 molecules BADC

#1: Protein Glucosyltransferase TcdA


Mass: 62918.996 Da / Num. of mol.: 2 / Mutation: K190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdA, toxA / Production host: Escherichia coli (E. coli)
References: UniProt: P16154, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Antibody Nanobody VHH AH3


Mass: 16113.987 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 358 molecules

#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium phosphate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→78.73 Å / Num. obs: 94481 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Net I/σ(I): 12.5 / Num. measured all: 328473
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.133.20.4391423544860.8850.2870.5272.395.6
11.5-78.733.30.02919395960.9990.020.03540.598.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OQ5

6oq5


Resolution: 2.1→67.57 Å / SU ML: 0.2988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2605 1987 2.11 %
Rwork0.218 92403 -
obs0.2189 94390 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10231 0 132 341 10704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011410533
X-RAY DIFFRACTIONf_angle_d0.983414245
X-RAY DIFFRACTIONf_chiral_restr0.05861618
X-RAY DIFFRACTIONf_plane_restr0.00791818
X-RAY DIFFRACTIONf_dihedral_angle_d16.43643797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.35121510.28486321X-RAY DIFFRACTION95.39
2.15-2.210.29241280.25636581X-RAY DIFFRACTION99.23
2.21-2.270.30721420.24726620X-RAY DIFFRACTION99.73
2.27-2.350.25961400.23766623X-RAY DIFFRACTION99.81
2.35-2.430.28491450.23446595X-RAY DIFFRACTION99.88
2.43-2.530.30941420.24286652X-RAY DIFFRACTION99.66
2.53-2.640.29281370.24446624X-RAY DIFFRACTION99.85
2.64-2.780.31541510.2496607X-RAY DIFFRACTION99.72
2.78-2.960.3031350.24436629X-RAY DIFFRACTION99.47
2.96-3.190.31521430.25036526X-RAY DIFFRACTION98.19
3.19-3.510.28031420.23556642X-RAY DIFFRACTION99.69
3.51-4.010.22991490.19566642X-RAY DIFFRACTION99.69
4.01-5.060.20651370.17066638X-RAY DIFFRACTION99.3
5.06-67.570.21741450.19286703X-RAY DIFFRACTION99.07

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