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- PDB-7s0z: Structures of TcdB in complex with R-Ras -

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Basic information

Entry
Database: PDB / ID: 7s0z
TitleStructures of TcdB in complex with R-Ras
Components
  • Ras-related protein R-Ras
  • Toxin B
KeywordsHydrolase/Transferase / toxin / substrate / enzyme / Hydrolase-Transferase complex
Function / homology
Function and homology information


leukocyte differentiation / positive regulation of endothelial cell-matrix adhesion / negative regulation of Schwann cell migration / Schwann cell migration / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of vasculogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D mediated inhibition of cell attachment and migration / face morphogenesis / host cell cytosol ...leukocyte differentiation / positive regulation of endothelial cell-matrix adhesion / negative regulation of Schwann cell migration / Schwann cell migration / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of vasculogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D mediated inhibition of cell attachment and migration / face morphogenesis / host cell cytosol / glycosyltransferase activity / regulation of ERK1 and ERK2 cascade / positive regulation of endothelial cell migration / cysteine-type peptidase activity / host cell endosome membrane / small monomeric GTPase / positive regulation of angiogenesis / GDP binding / toxin activity / Ras protein signal transduction / focal adhesion / GTPase activity / lipid binding / GTP binding / protein-containing complex binding / host cell plasma membrane / proteolysis / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization 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 ...Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization 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. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / : / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Glycosylating toxin TcdB / Ras-related protein R-Ras
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
B: Toxin B
A: Toxin B
C: Ras-related protein R-Ras
D: Ras-related protein R-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,42255
Polymers165,1754
Non-polymers4,24751
Water9,710539
1
B: Toxin B
D: Ras-related protein R-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,54023
Polymers82,5872
Non-polymers1,95321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-29 kcal/mol
Surface area30720 Å2
MethodPISA
2
A: Toxin B
C: Ras-related protein R-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,88232
Polymers82,5872
Non-polymers2,29530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-61 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.308, 112.112, 101.571
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules BACD

#1: Protein Toxin B


Mass: 62642.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, SAMEA708418_03270 / Production host: Escherichia coli (E. coli)
References: UniProt: M4NKV9, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein Ras-related protein R-Ras / p23


Mass: 19945.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAS / Production host: Escherichia coli (E. coli)
References: UniProt: P10301, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Sugars , 1 types, 2 molecules

#9: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 9 types, 588 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate, 0.1M sodium citrate tribasic dihydrate, pH 4.8, and 17% PEG 4000

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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 EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→112.11 Å / Num. obs: 70923 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.6
Reflection shellResolution: 2.34→2.39 Å / Num. unique obs: 4599 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OQ7,2FN4

6oq7

2fn4


Resolution: 2.34→76.02 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.499 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3516 5 %RANDOM
Rwork0.201 ---
obs0.203 67379 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å21.94 Å2
2---2.03 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.34→76.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11614 0 265 539 12418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01312073
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710958
X-RAY DIFFRACTIONr_angle_refined_deg1.231.65916305
X-RAY DIFFRACTIONr_angle_other_deg1.4591.58525529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18151438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11524.384666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.422152126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0441550
X-RAY DIFFRACTIONr_chiral_restr0.0620.21579
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022415
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_it1.3064.0285776
X-RAY DIFFRACTIONr_mcbond_other1.3064.0285775
X-RAY DIFFRACTIONr_mcangle_it2.176.0317196
X-RAY DIFFRACTIONr_mcangle_other2.176.0317197
X-RAY DIFFRACTIONr_scbond_it1.5374.1736297
X-RAY DIFFRACTIONr_scbond_other1.5384.1746289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.56.1969097
X-RAY DIFFRACTIONr_long_range_B_refined3.82747.73814103
X-RAY DIFFRACTIONr_long_range_B_other3.80447.65214025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 238 -
Rwork0.262 5019 -
obs--99.6 %

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