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- PDB-1ow3: Crystal Structure of RhoA.GDP.MgF3-in Complex with RhoGAP -

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Basic information

Entry
Database: PDB / ID: 1ow3
TitleCrystal Structure of RhoA.GDP.MgF3-in Complex with RhoGAP
Components
  • Rho-GTPase-activating protein 1
  • Transforming protein RhoA
KeywordsGENE REGULATION/SIGNALING PROTEIN / Complex / GTPase / GAP / transition state / GENE REGULATION-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of endocytic recycling / transferrin transport / 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 ...negative regulation of endocytic recycling / transferrin transport / 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 / RHOF GTPase cycle / RHO GTPases activate CIT / RHOD GTPase cycle / 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 / regulation of small GTPase mediated signal transduction / 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 / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / endosomal transport / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / RHOB GTPase cycle / small GTPase-mediated signal transduction / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ 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 / CDC42 GTPase cycle / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOG GTPase cycle / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / RAC3 GTPase cycle / RAC2 GTPase cycle / 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 / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / GTPase activator activity / substrate adhesion-dependent cell spreading / cell-matrix adhesion
Similarity search - Function
: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain ...: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Small GTPase Rho / small GTPase Rho family profile. / Rho GTPase activation protein / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / TRIFLUOROMAGNESATE / Transforming protein RhoA / Rho GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGraham, D.L. / Lowe, P.N. / Grime, G.W. / Marsh, M. / Rittinger, K. / Smerdon, S.J. / Gamblin, S.J. / Eccleston, J.F.
CitationJournal: Chem.Biol. / Year: 2002
Title: MgF(3)(-) as a Transition State Analog of Phosphoryl Transfer
Authors: Graham, D.L. / Lowe, P.N. / Grime, G.W. / Marsh, M. / Rittinger, K. / Smerdon, S.J. / Gamblin, S.J. / Eccleston, J.F.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-GTPase-activating protein 1
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7595
Polymers49,2112
Non-polymers5493
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-28 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.490, 71.400, 91.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Rho-GTPase-activating protein 1 / GTPase-activating protein rhoOGAP / Rho-related small GTPase protein activator / CDC42 GTPase- ...GTPase-activating protein rhoOGAP / Rho-related small GTPase protein activator / CDC42 GTPase-activating protein / p50-rhoGAP


Mass: 27444.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOGAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960
#2: Protein Transforming protein RhoA / / H12


Mass: 21766.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA / Production host: Escherichia coli (E. coli) / References: UniProt: P61586

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Non-polymers , 4 types, 377 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.2 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% PEG2KMME, 100mM MES, 10mM MgCl2, 10mM NaF, 2mM deferoxamine, 114mM (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.4 / Details: Rittinger, K., (1997) Nature, 389, 758.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 %PEG2000 MME1reservoir
2100 mMMES1reservoir
310 mM1reservoirMgCl2
43 mMdithiothreitol1reservoir
53 mM1reservoirNaN3
6114 mMammonium sulfate1reservoir
70.400 mMprotein1drop
820 mMTris-HCl1drop
91 mM1dropAlCl3
1010 mM1dropNaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 40798 / Num. obs: 40618 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rsym value: 0.083 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.401 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 99.6 % / Num. measured all: 218823 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.401

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TX4

1tx4


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.434 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.21893 2038 5 %RANDOM
Rwork0.18608 ---
obs0.18774 38536 99.68 %-
all-40618 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 33 374 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0263096
X-RAY DIFFRACTIONr_angle_refined_deg1.2262.0084214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2153373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15215572
X-RAY DIFFRACTIONr_chiral_restr0.0860.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022339
X-RAY DIFFRACTIONr_nbd_refined0.2450.31523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.325
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.520
X-RAY DIFFRACTIONr_mcbond_it0.6691.51882
X-RAY DIFFRACTIONr_mcangle_it1.29623067
X-RAY DIFFRACTIONr_scbond_it1.90431214
X-RAY DIFFRACTIONr_scangle_it3.3134.51147
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.241 161
Rwork0.233 2758
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / Rfactor Rwork: 0.205

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