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- PDB-8yvj: Crystal structure of the C. difficile toxin A CROPs domain fragme... -

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Basic information

Entry
Database: PDB / ID: 8yvj
TitleCrystal structure of the C. difficile toxin A CROPs domain fragment 2592-2710 bound to H5.2 nanobody
Components
  • H5.2 nanobody (VHH)
  • Toxin A
KeywordsTOXIN/IMMUNE SYSTEM / CROPs domain fragment / Toxin A / Complex with nanobody / Clostridioides difficile / TOXIN / TOXIN-IMMUNE SYSTEM complex
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
Similarity search - Domain/homology
PHOSPHATE ION / Toxin A
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Clostridioides difficile 342 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSluchanko, N.N. / Varfolomeeva, L.A. / Shcheblyakov, D.V. / Belyi, Y.F. / Logunov, D.Y. / Gintsburg, A.L. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural insight into recognition of Clostridioides difficile toxin A by novel neutralizing nanobodies targeting QTIN-like motifs within its receptor-binding domain.
Authors: Sluchanko, N.N. / Sokolova, I.V. / Favorskaya, I.A. / Esmagambetov, I.B. / Tukhvatulin, A.I. / Alekseeva, I.A. / Ungur, A.S. / Varfolomeeva, L.A. / Boyko, K.M. / Logunov, D.Y. / Gintsburg, A. ...Authors: Sluchanko, N.N. / Sokolova, I.V. / Favorskaya, I.A. / Esmagambetov, I.B. / Tukhvatulin, A.I. / Alekseeva, I.A. / Ungur, A.S. / Varfolomeeva, L.A. / Boyko, K.M. / Logunov, D.Y. / Gintsburg, A.L. / Popov, V.O. / Shcheblyakov, D.V. / Belyi, Y.F.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H5.2 nanobody (VHH)
B: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2034
Polymers27,0462
Non-polymers1572
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.156, 71.739, 93.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody H5.2 nanobody (VHH)


Mass: 13645.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
#2: Protein Toxin A


Mass: 13401.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 342 (bacteria)
Strain: VPI10463 / Gene: tcdA, toxA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium phosphate dibasic, pH 8.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→21.35 Å / Num. obs: 26488 / % possible obs: 98.5 % / Redundancy: 11.1 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.009 / Rrim(I) all: 0.032 / Χ2: 0.92 / Net I/σ(I): 54.1 / Num. measured all: 294560
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 82.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Num. measured all: 5072 / Num. unique obs: 1095 / CC1/2: 0.983 / Rpim(I) all: 0.055 / Rrim(I) all: 0.121 / Χ2: 0.98 / Net I/σ(I) obs: 12.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
CrysalisProdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→21.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.532 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19836 1304 4.9 %RANDOM
Rwork0.14871 ---
obs0.15108 25128 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0 Å2
2---0.12 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.65→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 9 351 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.041.7882657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.17559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68910307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1450.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021547
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1960.834990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9261.4881235
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1891.027975
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.97715.973196
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 86 -
Rwork0.159 1592 -
obs--84.92 %

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