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- PDB-7so5: Novel structural insights for a pair of monoclonal antibodies rec... -

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Basic information

Entry
Database: PDB / ID: 7so5
TitleNovel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B
Components
  • Fab B2 HC
  • Fab B2 LC
  • Toxin B
KeywordsTOXIN/IMMUNE SYSTEM / antibody / toxin / TcdB / epitope / Clostridium difficile toxin / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 / membrane / metal ion binding
Similarity search - Function
Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization 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 ...Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization 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 speciesHomo sapiens (human)
Clostridioides difficile R20291 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsLiu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B.
Authors: Liu, J. / Kothe, M. / Zhang, J. / Oloo, E. / Stegalkina, S. / Mundle, S.T. / Li, L. / Zhang, J. / Cole, L.E. / Barone, L. / Biemann, H.P. / Kleanthous, H. / Anosova, N.G. / Anderson, S.F.
History
DepositionOct 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab B2 HC
L: Fab B2 LC
A: Toxin B


Theoretical massNumber of molelcules
Total (without water)109,3663
Polymers109,3663
Non-polymers00
Water13,547752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.167, 110.722, 83.060
Angle α, β, γ (deg.)90.000, 99.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab B2 HC


Mass: 22844.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab B2 LC


Mass: 23554.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Toxin B


Mass: 62967.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile R20291 (bacteria)
Gene: tcdB, toxB / Production host: Escherichia coli (E. coli)
References: UniProt: P18177, Transferases; Glycosyltransferases; Hexosyltransferases
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.2 and 39% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.79→52.88 Å / Num. obs: 95088 / % possible obs: 93.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.82 Å2 / CC1/2: 0.998 / R split: 0.043 / Net I/σ(I): 14.9
Reflection shellResolution: 1.79→1.89 Å / Num. unique obs: 14702 / CC1/2: 0.996 / R split: 0.467

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVL

2bvl


Resolution: 1.797→52.867 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 4684 4.93 %
Rwork0.185 90359 -
obs0.1869 95043 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.22 Å2 / Biso mean: 30.8103 Å2 / Biso min: 13.68 Å2
Refinement stepCycle: final / Resolution: 1.797→52.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7684 0 0 752 8436
Biso mean---36.65 -
Num. residues----970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7974-1.81780.28631650.24833168100
1.8178-1.83920.30681800.24013169100
1.8392-1.86170.29471550.23683212100
1.8617-1.88520.28081730.23863173100
1.8852-1.910.28991450.2466282690
1.91-1.93620.3439420.233284975
1.9362-1.96390.28581710.21863169100
1.9639-1.99320.25931620.22243176100
1.9932-2.02430.25081840.20693196100
2.0243-2.05750.27111550.21553206100
2.0575-2.0930.29791100.2065226071
2.093-2.1310.28561720.20513201100
2.131-2.1720.22761450.1993250100
2.172-2.21640.21031620.19053168100
2.2164-2.26460.23131280.1915246677
2.2646-2.31720.26961480.19593199100
2.3172-2.37520.23811740.19183184100
2.3752-2.43940.24121770.19573200100
2.4394-2.51120.24971800.20423170100
2.5112-2.59220.25441520.20113194100
2.5922-2.68490.27421450.2044283388
2.6849-2.79240.22591510.1983321899
2.7924-2.91950.21681570.1993319699
2.9195-3.07340.24481490.2005322299
3.0734-3.26590.22951590.1944317499
3.2659-3.5180.21631760.1796297594
3.518-3.87190.23081670.1686291891
3.8719-4.4320.15071720.1455297392
4.432-5.58280.16551630.1466320499
5.5828-52.860.19691650.1589321098

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