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- PDB-7qsc: GTPase IN COMPLEX WITH GDP.MGF3- -

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Basic information

Entry
Database: PDB / ID: 7qsc
TitleGTPase IN COMPLEX WITH GDP.MGF3-
Components
  • Rho GTPase-activating protein 1
  • Transforming protein RhoA
KeywordsHYDROLASE / Small G Protein / GTPase / Transition state analogue / metal fluoride complexes / fluoro-tyrosine
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 / small GTPase-mediated signal transduction / RHOB GTPase cycle / 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
: / 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 ...: / 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 nucleoside triphosphate hydrolase
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: 1.91 Å
AuthorsBaumann, P. / Jin, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: GTPase IN COMPLEX WITH GDP.MGF3-
Authors: Baumann, P. / Jin, Y.
History
DepositionJan 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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
C: Rho GTPase-activating protein 1
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,48010
Polymers98,3834
Non-polymers1,0986
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, Observation of MgF3- transition state analog using 19F-NMR spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-44 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.765, 66.489, 76.958
Angle α, β, γ (deg.)90.000, 95.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 27502.482 Da / Num. of mol.: 2 / Mutation: R85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP1, CDC42GAP, RHOGAP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07960
#2: Protein Transforming protein RhoA / / Rho cDNA clone 12 / h12


Mass: 21688.863 Da / Num. of mol.: 2 / Mutation: Y34(F3Y)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61586, small monomeric GTPase

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Non-polymers , 4 types, 319 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0. ...Details: Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0.1 M BisTris-HCl, pH 5.8, PEG3350 26% (w/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.91→55.64 Å / Num. obs: 57691 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.085 / Rrim(I) all: 0.16 / Net I/σ(I): 10.4
Reflection shellResolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3865 / CC1/2: 0.649 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M6X

5m6x


Resolution: 1.91→55.64 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.572 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2945 2918 5.1 %RANDOM
Rwork0.2436 ---
obs0.2462 54747 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.99 Å2 / Biso mean: 28.051 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20.89 Å2
2---2.71 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.91→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5847 0 66 339 6252
Biso mean--22.89 30.99 -
Num. residues----730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155791
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.6348250
X-RAY DIFFRACTIONr_angle_other_deg1.1611.57613344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53323.585318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9281532
X-RAY DIFFRACTIONr_chiral_restr0.0640.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 197 -
Rwork0.377 4034 -
all-4231 -
obs--99.93 %

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