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- PDB-4xsg: The complex structure of C3cer exoenzyme and GTP bound RhoA (NADH... -

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Basic information

Entry
Database: PDB / ID: 4xsg
TitleThe complex structure of C3cer exoenzyme and GTP bound RhoA (NADH-free state)
Components
  • ADP-ribosyltransferase
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN/Transferase / ADP Ribose Transferases / Bacterial Toxins / SIGNALING PROTEIN-Transferase complex
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / apical junction assembly / regulation of modification of postsynaptic structure / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / negative regulation of cell size / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / Wnt signaling pathway, planar cell polarity pathway / odontogenesis / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / EPHA-mediated growth cone collapse / stress fiber assembly / positive regulation of cytokinesis / androgen receptor signaling pathway / myosin binding / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / mitotic spindle assembly / RHOA GTPase cycle / negative regulation of cell-substrate adhesion / positive regulation of T cell migration / endothelial cell migration / Rho protein signal transduction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / GPVI-mediated activation cascade / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / cell periphery / regulation of actin cytoskeleton organization / kidney development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / Ovarian tumor domain proteases / cell morphogenesis / neuron migration / G beta:gamma signalling through PI3Kgamma / cell junction
Similarity search - Function
Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Transforming protein RhoA / ADP-ribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToda, A. / Tsurumura, T. / Yoshida, T. / Tsuge, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research, MEXT of Japan25121733 Japan
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure.
Authors: Toda, A. / Tsurumura, T. / Yoshida, T. / Tsumori, Y. / Tsuge, H.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2126
Polymers45,5242
Non-polymers6884
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-14 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.745, 50.745, 135.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20235.180 Da / Num. of mol.: 1 / Fragment: UNP residues 1-179 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#2: Protein ADP-ribosyltransferase


Mass: 25288.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: c3cer / Plasmid: pRham / Production host: Escherichia coli DH10B (bacteria) / Strain (production host): DH10B / References: UniProt: Q8KNY0

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Non-polymers , 4 types, 312 molecules

#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES (pH 6.4), 20% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 36314 / % possible obs: 100 % / Redundancy: 5.7 % / Net I/σ(I): 39.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A2B, 3BW8

1a2b

3bw8


Resolution: 1.8→45.29 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.168 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22274 1808 5 %RANDOM
Rwork0.17483 ---
obs0.17714 34457 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 41 308 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023167
X-RAY DIFFRACTIONr_bond_other_d0.0020.023045
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9824266
X-RAY DIFFRACTIONr_angle_other_deg0.91837051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38724.932148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85615601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1421518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213498
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02680
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_it3.0832.8761522
X-RAY DIFFRACTIONr_mcbond_other3.0732.8751521
X-RAY DIFFRACTIONr_mcangle_it4.1134.2981899
X-RAY DIFFRACTIONr_mcangle_other4.1134.31900
X-RAY DIFFRACTIONr_scbond_it4.1373.3661645
X-RAY DIFFRACTIONr_scbond_other4.1373.3661645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1174.8372368
X-RAY DIFFRACTIONr_long_range_B_refined7.76628.21713417
X-RAY DIFFRACTIONr_long_range_B_other7.76628.21713417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 128 -
Rwork0.291 2539 -
obs--100 %
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)
10.3924-0.03590.14420.2962-0.08410.83390.0145-0.02980.033-0.06380.00290.03470.04960.0451-0.01740.07410.0075-0.02240.0256-0.00210.0547-0.3512-7.6174-28.7371
21.4584-0.26490.0660.10080.12160.7187-0.01380.14580.0176-0.0642-0.04710.0332-0.0159-0.10810.06090.1468-0.0039-0.06110.0423-0.00040.0543-10.7531-3.1487-38.2739
30.39610.2431-0.3171.0574-0.78411.6502-0.0103-0.10770.109-0.2049-0.0664-0.02380.35020.26440.07660.1280.05850.01060.066-0.02210.064210.2564-21.753-13.5117
40.29-0.3687-0.19040.49750.43261.48620.0040.0005-0.00370.0335-0.01560.01680.3419-0.08610.01170.1393-0.0121-0.02350.00820.00010.0507-3.1079-21.5817-7.9818
57.3674.301-3.95423.968-2.4342.1345-0.14560.03990.28370.30570.2919-0.03130.0438-0.0505-0.14630.13520.0381-0.05320.1220.01060.1211.0094-7.6018-12.4787
60.1721-0.2082-0.11810.86990.01681.06340.0355-0.00850.03660.0689-0.0191-0.01540.22840.1493-0.01630.14570.0411-0.01420.03760.00440.04326.4412-20.26-8.9849
71.4996-1.33670.55631.2806-0.06522.39530.02680.1655-0.006-0.0098-0.11970.0287-0.07160.16850.09290.1224-0.00790.02260.04290.02460.0428-4.3292-8.1995-1.7298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 114
2X-RAY DIFFRACTION2A115 - 179
3X-RAY DIFFRACTION3B15 - 61
4X-RAY DIFFRACTION4B62 - 146
5X-RAY DIFFRACTION5B147 - 155
6X-RAY DIFFRACTION6B156 - 196
7X-RAY DIFFRACTION7B197 - 219

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