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Basic information

Entry
Database: PDB / ID: 5ez6
TitleCrystallization and preliminary X-ray crystallographic analysis of a small GTPase RhoA
ComponentsTransforming protein RhoA
KeywordsSIGNALING PROTEIN / Nucleotide Binding / Gtpase Activity / Protein Binding / GTP Binding / GDP Binding
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway ...alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / odontogenesis / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / stress fiber assembly / positive regulation of leukocyte adhesion to vascular endothelial cell / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / regulation of focal adhesion assembly / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / ossification involved in bone maturation / EPHA-mediated growth cone collapse / apical junction complex / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / mitotic spindle assembly / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOA GTPase cycle / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / positive regulation of neuron differentiation / GPVI-mediated activation cascade / RHO GTPases activate PKNs / negative regulation of reactive oxygen species biosynthetic process / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoplasmic microtubule organization / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / secretory granule membrane / regulation of actin cytoskeleton organization / cell periphery / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of microtubule cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / ruffle membrane / actin cytoskeleton organization / Ovarian tumor domain proteases / cell migration / G beta:gamma signalling through PI3Kgamma / lamellipodium / G alpha (12/13) signalling events / cellular response to lipopolysaccharide / midbody / G protein activity / cell cortex / cytoskeleton / dendritic spine / vesicle / cytoplasmic side of plasma membrane / positive regulation of canonical NF-kappaB signal transduction / postsynapse / endosome / focal adhesion / GTPase activity / Neutrophil degranulation
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
GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYan, Z. / Ma, S. / Zhang, Y. / Ma, L. / Wang, F. / Li, J. / Miao, L.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China81202394 China
National Natural Science Foundation of China21222211 China
National Natural Science Foundation of China21372001 China
National Natural Science Foundation of China91313303 China
CitationJournal: To Be Published
Title: Crystallization and preliminary X-ray crystallographic analysis of a small GTPase RhoA
Authors: Yan, Z. / Ma, S. / Zhang, Y. / Ma, L. / Wang, F. / Li, J. / Miao, L.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9845
Polymers20,4671
Non-polymers5164
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-32 kcal/mol
Surface area9370 Å2
Unit cell
Length a, b, c (Å)91.407, 91.407, 56.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 20467.457 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P61586
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22677 / % possible obs: 100 % / Redundancy: 13.8 % / Net I/σ(I): 43.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.92 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21288 1159 5.1 %RANDOM
Rwork0.17734 ---
obs0.17908 21470 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.012 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 31 72 1522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191486
X-RAY DIFFRACTIONr_bond_other_d00.021405
X-RAY DIFFRACTIONr_angle_refined_deg1.4632.0022019
X-RAY DIFFRACTIONr_angle_other_deg0.75733254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4824.78369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47515262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8651510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
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_it1.9212.24720
X-RAY DIFFRACTIONr_mcbond_other1.912.239719
X-RAY DIFFRACTIONr_mcangle_it2.7093.35900
X-RAY DIFFRACTIONr_mcangle_other2.7133.35901
X-RAY DIFFRACTIONr_scbond_it2.8542.646765
X-RAY DIFFRACTIONr_scbond_other2.8672.655757
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2773.831107
X-RAY DIFFRACTIONr_long_range_B_refined5.77518.7781714
X-RAY DIFFRACTIONr_long_range_B_other5.77418.7781715
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
Rfree0.321 80 -
Rwork0.202 1545 -
obs--99.63 %

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