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- PDB-6way: C-terminal SH2 domain of p120RasGAP in complex with p190RhoGAP ph... -

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Basic information

Entry
Database: PDB / ID: 6way
TitleC-terminal SH2 domain of p120RasGAP in complex with p190RhoGAP phosphotyrosine peptide
Components
  • Ras GTPase-activating protein 1
  • Rho GTPase-activating protein 35
KeywordsSIGNALING PROTEIN / SH2 domain / RasGAP / phosphopeptide / phosphotyrosine
Function / homology
Function and homology information


neuron projection guidance / central nervous system neuron axonogenesis / regulation of RNA metabolic process / establishment or maintenance of actin cytoskeleton polarity / 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 / regulation of RNA metabolic process / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / : / regulation of actin filament polymerization / positive regulation of cilium assembly / mammary gland development / potassium channel inhibitor activity / camera-type eye development / negative regulation of cell adhesion / 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 / RND1 GTPase cycle / blood vessel morphogenesis / wound healing, spreading of cells / RND2 GTPase cycle / RND3 GTPase cycle / negative regulation of Rho protein signal transduction / regulation of cell size / RHOB GTPase cycle / regulation of axonogenesis / negative regulation of cell-matrix adhesion / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / mitotic cytokinesis / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / forebrain development / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / phosphotyrosine residue binding / GTPase activator activity / Downstream signal transduction / ciliary basal body / VEGFR2 mediated cell proliferation / neural tube closure / axon guidance / regulation of actin cytoskeleton organization / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / SHC Adaptor Protein / 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 / molecular replacement / Resolution: 1.5 Å
AuthorsJaber Chehayeb, R. / Wang, J. / Stiegler, A.L. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
American Heart Association19IPLOI34740007 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The GTPase-activating protein p120RasGAP has an evolutionarily conserved "FLVR-unique" SH2 domain.
Authors: Jaber Chehayeb, R. / Wang, J. / Stiegler, A.L. / Boggon, T.J.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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
V: Rho GTPase-activating protein 35


Theoretical massNumber of molelcules
Total (without water)13,4832
Polymers13,4832
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.119, 83.910, 54.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 12467.936 Da / Num. of mol.: 1 / Mutation: C372S, C402S
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) / Variant (production host): Rosetta / References: UniProt: P20936
#2: Protein/peptide Rho GTPase-activating protein 35 / Glucocorticoid receptor DNA-binding factor 1 / Glucocorticoid receptor repression factor 1 / GRF-1 ...Glucocorticoid receptor DNA-binding factor 1 / Glucocorticoid receptor repression factor 1 / GRF-1 / Rho GAP p190A / p190-A


Mass: 1014.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NRY4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M Sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.5
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 23209 / % possible obs: 100 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.031 / Rrim(I) all: 0.152 / Χ2: 1.015 / Net I/σ(I): 5.9 / Num. measured all: 492046
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.558.60.88722660.8060.2930.9380.79999.8
1.55-1.6213.20.87122870.8970.240.9050.825100
1.62-1.6917.80.81823170.9470.1950.8420.879100
1.69-1.7821.70.69522670.9740.1520.7110.978100
1.78-1.8923.50.5423000.9850.1140.5521.181100
1.89-2.0425.10.33523190.9910.0680.3411.119100
2.04-2.2425.50.25823140.9910.0520.2641.065100
2.24-2.5624.90.20323150.9940.0410.2071.01100
2.56-3.2326.10.14623670.9960.0290.1491.012100
3.23-3024.80.09324570.9980.0190.0951.004100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSB

2gsb


Resolution: 1.5→27.278 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.1903 1148 4.96 %
Rwork0.1645 --
obs0.1658 23164 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.96 Å2 / Biso mean: 27.7472 Å2 / Biso min: 13.82 Å2
Refinement stepCycle: final / Resolution: 1.5→27.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 197 1142
Biso mean---39.27 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051020
X-RAY DIFFRACTIONf_angle_d0.8091386
X-RAY DIFFRACTIONf_dihedral_angle_d16.946615
X-RAY DIFFRACTIONf_chiral_restr0.057135
X-RAY DIFFRACTIONf_plane_restr0.006188
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.503-1.57090.27771300.2477260695
1.5709-1.65370.2381450.22262713100
1.6537-1.75730.20411480.20112749100
1.7573-1.8930.191370.18232730100
1.893-2.08340.2061480.16142755100
2.0834-2.38470.19111440.16192765100
2.3847-3.00390.21051580.17372778100
3.0039-27.2780.16491380.14362920100
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)
16.8415-6.35534.25966.8024-6.01699.27640.2064-0.3776-0.6337-0.3310.24030.54970.5773-0.4614-0.43220.2078-0.0313-0.03120.28060.04860.254941.619617.690828.6766
22.818-3.6498-3.99916.47893.22668.277-0.2366-0.3991-0.27580.10210.22-0.08410.47620.34590.05330.1450.00870.00970.15920.02480.193141.596120.618.1366
34.9511-1.05610.4945.7534-1.90758.0709-0.0754-0.0052-0.2686-0.3776-0.0751-0.38280.60440.44570.12420.1760.01470.0450.1954-0.02280.185345.149719.62466.1197
41.272-1.3653-2.09455.8611-1.71146.6083-0.08020.2513-0.0727-0.12380.03080.0893-0.01120.0451-0.02290.0679-0.01250.01640.1155-0.00210.149540.45325.335110.4139
52.431-0.54393.27021.8303-1.37818.0731-0.00730.08330.02040.0798-0.1615-0.2903-0.08340.47920.14630.1326-0.00460.00390.20080.01990.206849.634526.543416.0764
69.45844.43545.90186.5544.70014.4437-0.07910.5533-0.1849-0.50250.1783-0.1127-0.3060.3628-0.09270.1310.02490.04170.18690.00890.152947.165530.78497.1925
77.5802-5.91093.22257.4276-0.38442.996-0.3155-0.95180.22211.47620.3874-0.57311.6383-0.3589-0.08480.3499-0.0297-0.04680.2655-0.0250.18849.464434.659629.6204
88.75574.2539-1.69895.1258-0.86422.02550.0135-0.16870.2413-0.01080.0778-0.0784-0.32950.0122-0.07610.2181-0.0181-0.00050.1789-0.01310.170646.570538.026722.5778
95.0001-0.48885.63389.6834-5.5799.3261-0.0197-0.35890.08780.46540.16790.3903-0.5045-0.3973-0.0980.14380.00290.05250.184-0.02030.174537.582835.972718.2678
109.64532.7965-1.75342.0544-0.18675.73850.05340.26490.6532-0.1993-0.02110.1822-0.6796-0.1689-0.05570.23850.03690.01720.19130.05090.20139.143438.64997.9516
117.8458-2.3741.40298.1643-0.8787.82680.0395-0.5574-1.10520.29630.16850.5840.8616-0.1819-0.25210.2604-0.01030.00330.23240.05360.334435.676220.971213.0413
129.7713-7.31816.147.278-6.22485.5762-0.17830.00540.26610.0556-0.0233-0.2268-0.23930.45050.15760.2832-0.02880.03680.3384-0.030.305751.010436.950512.439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 339 through 348 )A339 - 348
2X-RAY DIFFRACTION2chain 'A' and (resid 349 through 357 )A349 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 367 )A358 - 367
4X-RAY DIFFRACTION4chain 'A' and (resid 368 through 378 )A368 - 378
5X-RAY DIFFRACTION5chain 'A' and (resid 379 through 391 )A379 - 391
6X-RAY DIFFRACTION6chain 'A' and (resid 392 through 401 )A392 - 401
7X-RAY DIFFRACTION7chain 'A' and (resid 402 through 408 )A402 - 408
8X-RAY DIFFRACTION8chain 'A' and (resid 409 through 418 )A409 - 418
9X-RAY DIFFRACTION9chain 'A' and (resid 419 through 428 )A419 - 428
10X-RAY DIFFRACTION10chain 'A' and (resid 429 through 438 )A429 - 438
11X-RAY DIFFRACTION11chain 'A' and (resid 439 through 444 )A439 - 444
12X-RAY DIFFRACTION12chain 'V' and (resid 1086 through 1093 )V0

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