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- PDB-6pxc: N-Terminal SH2 domain of the p120RasGAP bound to a p190RhoGAP pho... -

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Basic information

Entry
Database: PDB / ID: 6pxc
TitleN-Terminal SH2 domain of the p120RasGAP bound to a p190RhoGAP phosphotyrosine peptide
Components
  • Ras GTPase-activating protein 1
  • phosphopeptide of p190RhoGAP
KeywordsSIGNALING PROTEIN / SH2 GTPase Activating Proteins Ras pathway SIGNALING PROTEIN Rho pathway
Function / homology
Function and homology information


neuron projection guidance / central nervous system neuron axonogenesis / establishment or maintenance of actin cytoskeleton polarity / regulation of RNA metabolic process / regulation of actin polymerization or depolymerization / : / regulation of actin filament polymerization / positive regulation of cilium assembly / mammary gland development / potassium channel inhibitor activity ...neuron projection guidance / central nervous system neuron axonogenesis / establishment or maintenance of actin cytoskeleton polarity / regulation of RNA metabolic process / regulation of actin polymerization or depolymerization / : / regulation of actin filament polymerization / positive regulation of cilium assembly / mammary gland development / potassium channel inhibitor activity / negative regulation of cell adhesion / camera-type eye development / RHOD GTPase cycle / negative regulation of vascular permeability / axonal fasciculation / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / blood vessel morphogenesis / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / wound healing, spreading of cells / negative regulation of Rho protein signal transduction / regulation of cell size / RHOB GTPase cycle / negative regulation of cell-matrix adhesion / regulation of axonogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / mitotic cytokinesis / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / RAC3 GTPase cycle / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / forebrain development / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / phosphotyrosine residue binding / Downstream signal transduction / GTPase activator activity / ciliary basal body / VEGFR2 mediated cell proliferation / neural tube closure / regulation of actin cytoskeleton organization / axon guidance / phospholipid binding / positive regulation of neuron projection development / Regulation of RAS by GAPs / cell migration / actin cytoskeleton / GTPase binding / regulation of cell shape / negative regulation of neuron apoptotic process / intracellular signal transduction / signaling receptor binding / GTPase activity / protein-containing complex binding / GTP binding / negative regulation of apoptotic process / signal transduction / DNA binding / nucleus / plasma membrane / cytosol / cytoplasm
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. / Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain ...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. / Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / SHC Adaptor Protein / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Small GTPase / Ras family / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ras GTPase-activating protein 1 / Rho GTPase-activating protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJaber Chehayeb, R. / Stiegler, A.L. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
CitationJournal: Plos One / Year: 2019
Title: Crystal structures of p120RasGAP N-terminal SH2 domain in its apo form and in complex with a p190RhoGAP phosphotyrosine peptide.
Authors: Jaber Chehayeb, R. / Stiegler, A.L. / Boggon, T.J.
History
DepositionJul 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID / _audit_author.name
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras GTPase-activating protein 1
U: phosphopeptide of p190RhoGAP


Theoretical massNumber of molelcules
Total (without water)13,8932
Polymers13,8932
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-3 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.190, 64.827, 87.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ras GTPase-activating protein 1 / RasGAP / Ras p21 protein activator / p120GAP


Mass: 12266.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASA1, GAP, RASA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P20936
#2: Protein/peptide phosphopeptide of p190RhoGAP


Mass: 1626.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NRY4*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M Sodium Malonate 0.1M Bis Tris 6.5 2% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 16868 / % possible obs: 100 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.039 / Rrim(I) all: 0.163 / Χ2: 1.151 / Net I/σ(I): 11.3 / Num. measured all: 265969
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.668.61.1116520.7330.3981.1820.91299.9
1.66-1.7211.51.20316780.8650.361.2570.99399.9
1.72-1.814.81.13316520.9250.2971.1731.1100
1.8-1.916.90.80616600.9580.1970.831.32399.9
1.9-2.0216.50.42916800.970.1070.4421.267100
2.02-2.1717.70.316680.9670.0730.3091.15799.9
2.17-2.3918.10.2516630.9780.060.2581.277100
2.39-2.7417.60.21117080.9840.0520.2171.171100
2.74-3.4518.40.16217070.9920.0390.1671.072100
3.45-5017.30.13518000.9940.0330.1391.061100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k44

4k44


Resolution: 1.6→43.62 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.06
RfactorNum. reflection% reflection
Rfree0.2097 845 5.02 %
Rwork0.1845 --
obs0.1858 16839 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.45 Å2 / Biso mean: 44.7464 Å2 / Biso min: 20.9 Å2
Refinement stepCycle: final / Resolution: 1.6→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 0 58 992
Biso mean---51.61 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6002-1.70040.28891380.2673254997
1.7004-1.83170.2691460.25272647100
1.8317-2.01610.25211370.23812654100
2.0161-2.30780.23381410.21172645100
2.3078-2.90750.27391390.21372685100
2.9075-43.620.17181440.15482814100
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)
16.7079-3.43384.06833.1863-2.54672.93580.1009-0.73660.1150.56480.48211.1680.5262-0.9844-0.28230.4635-0.05710.1480.2865-0.06550.530435.379320.369932.1872
24.25880.79311.30367.8529-1.13856.80320.1183-0.25420.61940.6125-0.22140.0211-0.47880.45550.14780.2536-0.03130.0370.1829-0.03120.28944.944124.289630.1731
39.18563.44521.18682.05492.28868.7638-0.24311.21770.6595-0.58340.38720.1948-0.30880.8044-0.01630.4259-0.021-0.02960.49740.08160.412638.137819.509116.9409
48.16412.8035-0.52077.98420.855.0682-0.038-0.01870.03550.20690.0351-0.15550.02310.2429-0.13660.2580.01590.02030.20130.01640.178146.306715.86427.3313
56.61150.2042-2.09424.87114.66135.3047-0.01890.5787-0.95190.5922-0.47250.73371.5222-1.37620.50250.5191-0.09860.00990.4413-0.06970.435135.90214.583427.0682
68.97130.6545-1.93665.0718-0.01728.63930.0933-0.3349-0.72920.506-0.1327-0.46680.08820.42080.04150.3357-0.0137-0.03850.22190.05580.215645.0868.722335.5747
77.82580.7406-4.3589.48352.5665.5515-0.0246-0.62740.76081.02920.04630.95920.0756-0.6424-0.16520.5752-0.03790.18790.3605-0.09280.403139.010624.2836.2284
83.7831.3058-1.19762.40771.07346.90430.2160.56550.2126-0.3101-0.2070.25720.3410.359-0.13540.32550.04120.01640.39820.01790.377648.623514.007820.0677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 174 through 187 )A174 - 187
2X-RAY DIFFRACTION2chain 'A' and (resid 188 through 208 )A188 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 215 )A209 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 235 )A216 - 235
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 248 )A236 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 268 )A249 - 268
7X-RAY DIFFRACTION7chain 'A' and (resid 269 through 277 )A269 - 277
8X-RAY DIFFRACTION8chain 'U' and (resid 1100 through 1111 )U0

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