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

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Basic information

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


aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / 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 ...aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / 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 / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / skeletal muscle tissue development / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / cytoplasmic side of plasma membrane / ruffle membrane / VEGFA-VEGFR2 Pathway / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events
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 family 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 family 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Transforming protein RhoA / ADP-ribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)46,9398
Polymers45,5242
Non-polymers1,4156
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-17 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.424, 50.424, 136.667
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 / Poly (ADP-ribose) polymerase


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 , 5 types, 61 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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13464 / % possible obs: 99.9 % / Redundancy: 5.5 % / Net I/σ(I): 21

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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 and 3BW8

1a2b

3bw8


Resolution: 2.5→45.56 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 27.386 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25353 1334 9.9 %RANDOM
Rwork0.1895 ---
obs0.19589 12085 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 89 55 3218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023223
X-RAY DIFFRACTIONr_bond_other_d0.0030.023078
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9994348
X-RAY DIFFRACTIONr_angle_other_deg1.09837128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03524.932148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.00515601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3291518
X-RAY DIFFRACTIONr_chiral_restr0.0510.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213532
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02694
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_it2.9854.6491526
X-RAY DIFFRACTIONr_mcbond_other2.9834.6481525
X-RAY DIFFRACTIONr_mcangle_it4.5466.9731904
X-RAY DIFFRACTIONr_mcangle_other4.5456.9741905
X-RAY DIFFRACTIONr_scbond_it3.6395.2181697
X-RAY DIFFRACTIONr_scbond_other3.6395.2181697
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.747.6532445
X-RAY DIFFRACTIONr_long_range_B_refined8.90944.89913440
X-RAY DIFFRACTIONr_long_range_B_other8.90944.90213441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 95 -
Rwork0.327 902 -
obs--99.9 %
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)
11.7592-0.22870.60840.9755-0.04853.47020.0844-0.1836-0.02140.1224-0.195-0.0366-0.2251-0.02950.11060.1297-0.0791-0.01290.12530.00530.0757-6.407425.151828.2164
22.7804-1.1291-0.19452.3884-0.34713.3498-0.0429-0.6435-0.2420.3017-0.1299-0.12190.18070.53140.17280.1465-0.0489-0.05840.28880.1310.12432.870318.329537.6187
32.10541.1488-0.94133.2276-0.42984.06450.0102-0.24990.31930.07020.05420.0435-0.1199-0.5832-0.06440.00830.0071-0.01770.30890.02730.1198-24.09727.769612.7864
42.3277-0.1564-0.41110.997-0.21123.1227-0.10550.0703-0.1214-0.13080.13280.0470.4251-0.3282-0.02730.1107-0.0914-0.01080.1341-0.00010.1053-17.591416.1727.1723
50.05660.13440.43681.0763.04628.7071-0.1140.0085-0.06770.12030.3617-0.04750.16930.9658-0.24770.45330.13360.1220.1810.10630.278-8.417925.981511.4855
62.7666-0.09040.20261.1050.38353.4438-0.07520.03180.2425-0.07640.09250.10440.0263-0.4982-0.01740.0484-0.0366-0.01250.21650.03060.1001-20.937525.08888.1867
74.5415-0.30912.86722.3066-0.48612.9745-0.22420.33090.03040.01650.1595-0.10230.11410.19390.06470.1531-0.06560.07360.1808-0.03510.069-5.323121.67730.8309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 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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