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- PDB-5irc: p190A GAP domain complex with RhoA -

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Basic information

Entry
Database: PDB / ID: 5irc
Titlep190A GAP domain complex with RhoA
Components
  • Rho GTPase-activating protein 35
  • Transforming protein RhoA
KeywordsPROTEIN BINDING / protein-protein complex / transition state / GTPase / GAP domain
Function / homology
Function and homology information


Sema4D mediated inhibition of cell attachment and migration / : / RHOJ GTPase cycle / : / RND2 GTPase cycle / RND1 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOB GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle ...Sema4D mediated inhibition of cell attachment and migration / : / RHOJ GTPase cycle / : / RND2 GTPase cycle / RND1 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOB GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RND3 GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / central nervous system neuron axonogenesis / neuron projection guidance / establishment or maintenance of actin cytoskeleton polarity / RHOA GTPase cycle / regulation of actin polymerization or depolymerization / 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 / positive regulation of cilium assembly / forebrain radial glial cell differentiation / mammary gland development / 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 / negative regulation of cell size / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / camera-type eye development / negative regulation of vascular permeability / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / axonal fasciculation / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / GTPase activating protein binding / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / negative regulation of Rho protein signal transduction / apical junction complex / regulation of neuron projection development / regulation of focal adhesion assembly / negative chemotaxis / regulation of cell size / regulation of axonogenesis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cerebral cortex cell migration / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases
Similarity search - Function
Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein ...Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / 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 35
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsDerewenda, U. / Derewenda, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM086457 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Deciphering the Molecular and Functional Basis of RHOGAP Family Proteins: A SYSTEMATIC APPROACH TOWARD SELECTIVE INACTIVATION OF RHO FAMILY PROTEINS.
Authors: Amin, E. / Jaiswal, M. / Derewenda, U. / Reis, K. / Nouri, K. / Koessmeier, K.T. / Aspenstrom, P. / Somlyo, A.V. / Dvorsky, R. / Ahmadian, M.R.
History
DepositionMar 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho GTPase-activating protein 35
F: Transforming protein RhoA
B: Rho GTPase-activating protein 35
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,45813
Polymers88,2544
Non-polymers1,2049
Water18,3571019
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A: Rho GTPase-activating protein 35
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7477
Polymers44,1272
Non-polymers6205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-39 kcal/mol
Surface area16580 Å2
MethodPISA
2
B: Rho GTPase-activating protein 35
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7126
Polymers44,1272
Non-polymers5844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-40 kcal/mol
Surface area16030 Å2
MethodPISA
3
A: Rho GTPase-activating protein 35
F: Transforming protein RhoA
hetero molecules

B: Rho GTPase-activating protein 35
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,45813
Polymers88,2544
Non-polymers1,2049
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area9100 Å2
ΔGint-97 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.026, 112.322, 147.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABFD

#1: Protein Rho GTPase-activating protein 35 / GAP-associated protein p190 / Glucocorticoid receptor DNA-binding factor 1


Mass: 23307.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgap35, Grlf1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81128
#2: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20819.760 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) / Strain (production host): BL21(DE3) / References: UniProt: P61586

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Non-polymers , 5 types, 1028 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-GDP / GUANOSINE-5'-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


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


Mass: 18.015 Da / Num. of mol.: 1019 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsResidue 20 in chain F is an oxidized Cys (CSX). However, in chain D, the electron density does not ...Residue 20 in chain F is an oxidized Cys (CSX). However, in chain D, the electron density does not support the oxidation of the CYS residue.

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5 / Details: 30% PEG 2000MME 150mM KCSN 100mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→35 Å / Num. obs: 81511 / % possible obs: 97 % / Redundancy: 5.6 % / Biso Wilson estimate: 19.72 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.037 / Net I/av σ(I): 26.246 / Net I/σ(I): 12.6 / Num. measured all: 459261
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.72-1.752.60.36729150.90470
1.75-1.783.20.3534260.91183.3
1.78-1.8240.34437790.99190.9
1.82-1.854.60.30540261.01997.8
1.85-1.895.20.27941111.08798.1
1.89-1.945.50.23941141.16499.7
1.94-1.995.80.20341141.12999.4
1.99-2.045.90.1742071.162100
2.04-2.160.14941331.24799.8
2.1-2.176.20.1241751.152100
2.17-2.246.20.10241911.081100
2.24-2.336.20.08941711.027100
2.33-2.446.30.0741621.002100
2.44-2.576.30.06341970.963100
2.57-2.736.30.05942211.038100
2.73-2.946.30.05942311.072100
2.94-3.246.30.04442130.922100
3.24-3.76.20.03442820.881100
3.7-4.676.10.03443260.903100
4.67-355.90.04945170.93999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SERGUIdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→32.538 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1620 1.99 %Random selection
Rwork0.1703 79805 --
obs0.1712 81425 96.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.44 Å2 / Biso mean: 26.5312 Å2 / Biso min: 1.93 Å2
Refinement stepCycle: final / Resolution: 1.72→32.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5850 0 69 1019 6938
Biso mean--16.86 36.62 -
Num. residues----738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076048
X-RAY DIFFRACTIONf_angle_d1.1528205
X-RAY DIFFRACTIONf_chiral_restr0.044915
X-RAY DIFFRACTIONf_plane_restr0.0061051
X-RAY DIFFRACTIONf_dihedral_angle_d13.782251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7201-1.78160.26861260.2256200632676
1.7816-1.85290.26331530.2067646779994
1.8529-1.93730.24691540.19828074822899
1.9373-2.03940.2391680.182381458313100
2.0394-2.16710.25271490.171481558304100
2.1671-2.33440.20981720.167681948366100
2.3344-2.56920.26391830.174381718354100
2.5692-2.94080.21171640.180582818445100
2.9408-3.70430.21221800.160883008480100
3.7043-32.54430.16031710.153986398810100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1818-0.35370.36611.4144-0.68632.7029-0.03040.02150.03740.07470.03860.0227-0.1323-0.06310.01050.0418-0.0088-0.00110.08770.01090.087516.424169.17723.2618
21.15090.5741-0.48332.0746-0.85512.5667-0.00440.04240.0335-0.06610.04590.01990.0905-0.08080.01910.03270.0029-0.00060.0975-0.00470.084421.654147.214264.7941
31.57381.1153-0.88783.1702-1.14291.74030.09620.0940.39040.45010.12020.552-0.3744-0.17510.12820.21920.04140.05820.13130.02490.2719.422274.786562.1032
41.6083-0.00270.17372.26380.09382.89940.0811-0.0564-0.2030.0507-0.0840.01230.6912-0.18550.03860.2633-0.1187-0.02580.07510.02390.102914.410642.699632.2844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1241:1438))A0
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1243:1437))B0
3X-RAY DIFFRACTION3chain 'D' and ((resseq 4:180))D4 - 180
4X-RAY DIFFRACTION4chain 'F' and ((resseq 4:180))F4 - 180

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