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

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Basic information

Entry
Database: PDB / ID: 8yvo
TitleCrystal structure of the C. difficile toxin A CROPs domain fragment 2639-2707 bound to C4.2 nanobody
Components
  • C4.2 nanobody
  • 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


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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, 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 / 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. / 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
Biological speciesCamelus dromedarius (Arabian camel)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: C4.2 nanobody
B: C4.2 nanobody
C: Toxin A
D: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,97012
Polymers52,4734
Non-polymers4978
Water6,305350
1
A: C4.2 nanobody
C: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5477
Polymers26,2372
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C4.2 nanobody
D: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4235
Polymers26,2372
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.804, 42.850, 178.277
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Antibody C4.2 nanobody


Mass: 18550.719 Da / Num. of mol.: 2
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: 7685.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (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.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.4M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.9141
pseudo-merohedral22-h,-k,l20.0859
ReflectionResolution: 2.1→20.42 Å / Num. obs: 50005 / % possible obs: 98.6 % / Redundancy: 4 % / CC1/2: 0.984 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.082 / Rrim(I) all: 0.167 / Χ2: 1.02 / Net I/σ(I): 8.4 / Num. measured all: 197585
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 96.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.812 / Num. measured all: 16485 / Num. unique obs: 3980 / CC1/2: 0.609 / Rpim(I) all: 0.446 / Rrim(I) all: 0.929 / Χ2: 0.97 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.543 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23839 2501 5 %RANDOM
Rwork0.20986 ---
obs0.21128 47501 79.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.912 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å2-0 Å2-0.7 Å2
2--7.21 Å20 Å2
3----10.16 Å2
Refinement stepCycle: 1 / Resolution: 2.1→20.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 32 350 3394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123142
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162900
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.7984224
X-RAY DIFFRACTIONr_angle_other_deg0.7881.7446627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0745388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.122521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6910488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023807
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02825
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_it2.822.1111564
X-RAY DIFFRACTIONr_mcbond_other2.8192.111564
X-RAY DIFFRACTIONr_mcangle_it3.9943.7821948
X-RAY DIFFRACTIONr_mcangle_other3.9943.7831949
X-RAY DIFFRACTIONr_scbond_it3.1862.2791578
X-RAY DIFFRACTIONr_scbond_other3.1852.281579
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4864.0822277
X-RAY DIFFRACTIONr_long_range_B_refined6.28120.873443
X-RAY DIFFRACTIONr_long_range_B_other6.17620.663378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %
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)
10.4597-0.10720.45770.2498-0.06731.40.01370.0879-0.04470.05420.0141-0.03610.1104-0.0312-0.02780.0790.00080.00930.0688-0.01880.021911.9597-26.50414.6514
20.81760.1829-0.59510.1940.14261.35380.016-0.07840.0536-0.0436-0.0062-0.0174-0.0764-0.0244-0.00970.07930.00340.05760.0672-0.0170.055114.2487-17.5954-16.869
30.44590.38230.27071.0399-0.56091.06090.01570.0278-0.0289-0.01510.04440.00390.0127-0.0096-0.06010.11050.0149-0.01440.0043-0.00240.035322.0719-23.895140.5614
40.26360.0101-0.38160.8847-0.38990.78770.0182-0.0250.0284-0.00530.02030.02540.0129-0.0032-0.03860.1108-0.00920.08550.0156-0.0010.071428.017-20.1345-41.0667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 202
2X-RAY DIFFRACTION2B23 - 201
3X-RAY DIFFRACTION3C2639 - 2802
4X-RAY DIFFRACTION4D2639 - 2801

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