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- PDB-7s0y: Structures of TcdB in complex with Cdc42 -

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Basic information

Entry
Database: PDB / ID: 7s0y
TitleStructures of TcdB in complex with Cdc42
Components
  • Cell division control protein 42 homolog
  • Toxin B
KeywordsHYDROLASE / toxin / substrate / enzyme
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole ...GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / glucosyltransferase activity / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of lamellipodium assembly / regulation of stress fiber assembly / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / macrophage differentiation / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cysteine-type peptidase activity / host cell endosome membrane / secretory granule / actin filament organization / small monomeric GTPase / positive regulation of DNA replication / integrin-mediated signaling pathway / filopodium / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / RHO GTPases Activate Formins / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / G beta:gamma signalling through CDC42 / endocytosis
Similarity search - Function
Cdc42 / 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 ...Cdc42 / 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. / Small GTPase Rho / Small GTPase Rho domain profile. / Nucleotide-diphospho-sugar transferases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / URIDINE-5'-DIPHOSPHATE / Toxin B / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsZheng, L. / Rongsheng, J. / Peng, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B.
Authors: Liu, Z. / Zhang, S. / Chen, P. / Tian, S. / Zeng, J. / Perry, K. / Dong, M. / Jin, R.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 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
A: Toxin B
B: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,92117
Polymers82,9372
Non-polymers1,98315
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-181 kcal/mol
Surface area31600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.354, 140.948, 111.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Toxin B


Mass: 63026.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Production host: Escherichia coli (E. coli)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 19910.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953, small monomeric GTPase

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Non-polymers , 6 types, 38 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate (pH 6.6), 2.4 M ammonium sulfate, and 2.5% (v/v) Jeffamine M-600 (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→111.8 Å / Num. obs: 24433 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.9
Reflection shellResolution: 2.79→2.94 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3527 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVM

2bvm


Resolution: 2.79→92.4 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 17.558 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25924 1241 5.1 %RANDOM
Rwork0.21437 ---
obs0.21666 23173 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.173 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--4.68 Å20 Å2
3----2.86 Å2
Refinement stepCycle: 1 / Resolution: 2.79→92.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5787 0 110 23 5920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135998
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175373
X-RAY DIFFRACTIONr_angle_refined_deg1.311.6568136
X-RAY DIFFRACTIONr_angle_other_deg1.1591.58112539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72124.809314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.801151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.11520
X-RAY DIFFRACTIONr_chiral_restr0.0510.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
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_it4.5248.2552886
X-RAY DIFFRACTIONr_mcbond_other4.5128.2532885
X-RAY DIFFRACTIONr_mcangle_it6.99412.3783604
X-RAY DIFFRACTIONr_mcangle_other6.99612.3813605
X-RAY DIFFRACTIONr_scbond_it4.1988.5733112
X-RAY DIFFRACTIONr_scbond_other4.1248.5223060
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4612.6464454
X-RAY DIFFRACTIONr_long_range_B_refined9.51495.0886627
X-RAY DIFFRACTIONr_long_range_B_other9.51795.1046621
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 84 -
Rwork0.298 1715 -
obs--99.94 %

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