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- PDB-5m6x: Crystal Structure of human RhoGAP mutated in its arginine finger ... -

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Basic information

Entry
Database: PDB / ID: 5m6x
TitleCrystal Structure of human RhoGAP mutated in its arginine finger (R85A) in complex with RhoA.GDP.MgF3- human
Components
  • Rho GTPase-activating protein 1
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / RHOGAP / Arginine finger / RHOA / transition state
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
: / 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: 2.4 Å
AuthorsPellegrini, E. / Bowler, M.W.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, (19) F NMR, and DFT Approaches.
Authors: Jin, Y. / Molt, R.W. / Pellegrini, E. / Cliff, M.J. / Bowler, M.W. / Richards, N.G.J. / Blackburn, G.M. / Waltho, J.P.
History
DepositionOct 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / diffrn_radiation_wavelength / 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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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

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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
H: Rho GTPase-activating protein 1
I: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,74410
Polymers97,6464
Non-polymers1,0986
Water3,297183
1
A: Rho GTPase-activating protein 1
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3725
Polymers48,8232
Non-polymers5493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-26 kcal/mol
Surface area16140 Å2
MethodPISA
2
H: Rho GTPase-activating protein 1
I: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3725
Polymers48,8232
Non-polymers5493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-29 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.470, 66.690, 76.890
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules AHBI

#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: 27188.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP1, CDC42GAP, RHOGAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960
#2: Protein Transforming protein RhoA / / Rho cDNA clone 12 / h12


Mass: 21634.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61586

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Non-polymers , 4 types, 189 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: 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 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 100 mM Bis Tris pH 5.5-6.5 20-25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.4→40.29 Å / Num. obs: 23276 / % possible obs: 84.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 5.3
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.661

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W30

1w30


Resolution: 2.4→76.55 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.857 / SU B: 12.05 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27197 1260 5.1 %RANDOM
Rwork0.22425 ---
obs0.22666 23276 84.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å2-0 Å21.6 Å2
2---2.06 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.4→76.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 66 183 6087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196047
X-RAY DIFFRACTIONr_bond_other_d0.0010.025817
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.988224
X-RAY DIFFRACTIONr_angle_other_deg0.879313391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0275728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02225.017289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.878151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7921533
X-RAY DIFFRACTIONr_chiral_restr0.060.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021348
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_it0.5942.4352927
X-RAY DIFFRACTIONr_mcbond_other0.5942.4342926
X-RAY DIFFRACTIONr_mcangle_it1.1083.6463650
X-RAY DIFFRACTIONr_mcangle_other1.1083.6473651
X-RAY DIFFRACTIONr_scbond_it0.3622.4723120
X-RAY DIFFRACTIONr_scbond_other0.3622.4763106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7133.6744556
X-RAY DIFFRACTIONr_long_range_B_refined2.10618.526753
X-RAY DIFFRACTIONr_long_range_B_other2.05818.5376712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 107 -
Rwork0.29 1777 -
obs--87.51 %

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