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- PDB-3tvd: Crystal Structure of Mouse RhoA-GTP complex -

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Basic information

Entry
Database: PDB / ID: 3tvd
TitleCrystal Structure of Mouse RhoA-GTP complex
ComponentsTransforming protein RhoA
KeywordsSIGNALING PROTEIN / Alpha helical / Protein_GTP complex / Helical protein / GTP binding protein / Regulates signal transduction pathway / GTP / Nil / Membrane
Function / homology
Function and homology information


EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility / RHO GTPases activate KTN1 / PI3K/AKT activation ...EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility / RHO GTPases activate KTN1 / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Ovarian tumor domain proteases / Sema4D induced cell migration and growth-cone collapse / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / VEGFA-VEGFR2 Pathway / GPVI-mediated activation cascade / RHO GTPases Activate Formins / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / G alpha (12/13) signalling events / spindle localization / negative regulation of synapse assembly / RHO GTPases activate CIT / polar body extrusion after meiotic divisions / RHOA GTPase cycle / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / cellular response to progesterone stimulus / regulation of dendrite development / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / 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 / positive regulation of smooth muscle contraction / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / EPHB-mediated forward signaling / meiotic spindle organization / forebrain radial glial cell differentiation / regulation of modification of postsynaptic structure / cell junction assembly / apical junction assembly / embryonic cleavage / 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 / stress-activated protein kinase signaling cascade / G beta:gamma signalling through PI3Kgamma / negative regulation of cell size / positive regulation of podosome assembly / GTP metabolic process / positive regulation of alpha-beta T cell differentiation / meiotic spindle / apolipoprotein A-I-mediated signaling pathway / microtubule depolymerization / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / odontogenesis / motor neuron apoptotic process / ossification involved in bone maturation / Neutrophil degranulation / negative chemotaxis / apical junction complex / negative regulation of neuron differentiation / stress fiber assembly / androgen receptor signaling pathway / Rho GDP-dissociation inhibitor binding / myosin binding / positive regulation of cytokinesis / negative regulation of vascular associated smooth muscle cell migration / positive regulation of vasoconstriction / regulation of neuron projection development / positive regulation of actin filament polymerization / cellular response to cytokine stimulus / cerebral cortex cell migration / semaphorin-plexin signaling pathway / regulation of calcium ion transport / cleavage furrow / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / mitotic spindle assembly / response to amino acid / response to mechanical stimulus / positive regulation of T cell migration / endothelial cell migration / response to glucose / skeletal muscle tissue development
Similarity search - Function
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 / Rossmann fold ...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 / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.989 Å
AuthorsSwaminathan, K. / Pal, K. / Jobichen, C.
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Crystal structure of mouse RhoA:GTPgammaS complex in a centered lattice.
Authors: Jobichen, C. / Pal, K. / Swaminathan, K.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming protein RhoA
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7536
Polymers43,6262
Non-polymers1,1274
Water61334
1
A: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3773
Polymers21,8131
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3773
Polymers21,8131
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.813, 122.652, 91.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:181 )
211CHAIN B AND (RESSEQ 6:181 )

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Components

#1: Protein Transforming protein RhoA


Mass: 21813.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arha, Arha2, Rhoa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61589
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate (pH4.6), 30% Polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 21, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.989→29 Å / Num. all: 8595 / Num. obs: 8595 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.16
Reflection shellResolution: 3→3.15 Å / Redundancy: 4.9 % / Rsym value: 0.34 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTN

1ftn


Resolution: 2.989→14.999 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 853 9.92 %RANDOM
Rwork0.2226 ---
all0.2284 8595 --
obs0.2284 8595 91.27 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.69 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.3504 Å2-0 Å20 Å2
2---0.7651 Å20 Å2
3---11.1155 Å2
Refinement stepCycle: LAST / Resolution: 2.989→14.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 66 34 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092972
X-RAY DIFFRACTIONf_angle_d1.134041
X-RAY DIFFRACTIONf_dihedral_angle_d19.4261139
X-RAY DIFFRACTIONf_chiral_restr0.072446
X-RAY DIFFRACTIONf_plane_restr0.004519
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1398X-RAY DIFFRACTIONPOSITIONAL
12B1398X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9895-3.17510.39531340.2956122688
3.1751-3.41760.30791290.2594119686
3.4176-3.75660.36361350.2921122287
3.7566-4.2890.27761400.2052126690
4.289-5.36240.23461540.172136696
5.3624-14.99870.18951610.176146699

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