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- PDB-5bwm: The complex structure of C3cer exoenzyme and GDP bound RhoA (NADH... -

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Basic information

Entry
Database: PDB / ID: 5bwm
TitleThe complex structure of C3cer exoenzyme and GDP bound RhoA (NADH-bound 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 / regulation of modification of postsynaptic structure / cell junction assembly / apical 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 CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / stress fiber assembly / androgen receptor signaling pathway / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / GPVI-mediated activation cascade / Rho protein signal transduction / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / neuron migration / cell morphogenesis / Ovarian tumor domain proteases / cell junction / G beta:gamma signalling through PI3Kgamma
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
GUANOSINE-5'-DIPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Transforming protein RhoA / ADP-ribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionJun 8, 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 19, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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)46,7817
Polymers45,5242
Non-polymers1,2575
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-20 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.479, 50.479, 136.671
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 , 5 types, 60 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#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


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / 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: 2.29 Å3/Da / Density % sol: 46.38 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13477 / % possible obs: 99.6 % / Redundancy: 4.7 % / Net I/σ(I): 17.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.81 / % possible all: 100

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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: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 27.71 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24596 665 4.9 %RANDOM
Rwork0.20926 ---
obs0.21103 12780 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 81 55 3210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023216
X-RAY DIFFRACTIONr_bond_other_d0.0050.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9974339
X-RAY DIFFRACTIONr_angle_other_deg1.34237117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8135380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31724.932148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.40515601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5681518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213532
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02694
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_it3.1254.3141526
X-RAY DIFFRACTIONr_mcbond_other3.1264.3121525
X-RAY DIFFRACTIONr_mcangle_it4.8396.461904
X-RAY DIFFRACTIONr_mcangle_other4.8386.4621905
X-RAY DIFFRACTIONr_scbond_it3.4194.8031690
X-RAY DIFFRACTIONr_scbond_other3.4124.8031690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3467.0582436
X-RAY DIFFRACTIONr_long_range_B_refined9.40441.7613635
X-RAY DIFFRACTIONr_long_range_B_other9.40441.76213636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 41 -
Rwork0.386 987 -
obs--99.81 %
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)
10.4168-0.0968-0.21240.26910.58362.82430.0665-0.0769-0.0316-0.01-0.1435-0.05770.0596-0.09750.07690.1695-0.0218-0.03660.22-0.02540.5522-6.54425.270728.1989
22.9695-1.5612-0.43251.57190.82030.935-0.0207-0.5164-0.12030.32090.05290.120.38690.1315-0.03220.24540.0077-0.06670.31460.04680.45062.935418.59537.6816
31.80581.6421-0.36362.10151.16314.1453-0.0881-0.18620.099-0.1312-0.32950.101-0.1632-0.58580.41760.03250.1037-0.04920.3632-0.06260.5333-24.211927.489312.8633
42.28010.346-0.33640.11750.27762.2382-0.1958-0.22940.0072-0.0015-0.0857-0.01560.4699-0.31580.28150.2745-0.04420.04960.179-0.0320.5207-17.703715.99867.2726
50.6661-1.6517-0.75264.28852.88386.502-0.0772-0.0410.01880.13930.0947-0.01720.02940.0642-0.01740.2582-0.0062-0.01420.30490.03060.4199-8.598825.826611.5246
61.0157-0.25270.61230.76760.83412.3753-0.0665-0.27560.2212-0.2327-0.036-0.0947-0.0304-0.45380.10250.3016-0.0123-0.03620.2855-0.03410.5413-21.140424.80798.2168
75.38730.67782.89550.59330.77563.2045-0.4313-0.13960.132-0.15540.26740.00350.1060.04430.16390.33790.01310.06590.2349-0.02730.3999-5.485321.50850.5912
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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