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- PDB-8dgq: Crystal structure of p120RasGAP SH2-SH3-SH2 in complex with p190R... -

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Basic information

Entry
Database: PDB / ID: 8dgq
TitleCrystal structure of p120RasGAP SH2-SH3-SH2 in complex with p190RhoGAP doubly phosphorylated peptide
Components
  • Ras GTPase-activating protein 1
  • Rho GTPase-activating protein 35
KeywordsSIGNALING PROTEIN / SH2 domain / SH3 domain / phosphotyrosine
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 / 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
Similarity search - Domain/homology
MALONATE ION / 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: 1.95 Å
AuthorsStiegler, A.L. / Vish, K.J. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS117609 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138411 United States
CitationJournal: Structure / Year: 2022
Title: Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP.
Authors: Stiegler, A.L. / Vish, K.J. / Boggon, T.J.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Ras GTPase-activating protein 1
B: Ras GTPase-activating protein 1
U: Rho GTPase-activating protein 35
V: Rho GTPase-activating protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3447
Polymers70,0384
Non-polymers3063
Water4,197233
1
A: Ras GTPase-activating protein 1
U: Rho GTPase-activating protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2234
Polymers35,0192
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-13 kcal/mol
Surface area15970 Å2
MethodPISA
2
B: Ras GTPase-activating protein 1
V: Rho GTPase-activating protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1213
Polymers35,0192
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-9 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.210, 113.500, 119.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))
21(chain B and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPHEPHE(chain A and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))AA173 - 3902 - 219
12THRTHRPHEPHE(chain A and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))AA392 - 409221 - 238
13METMETMETMET(chain A and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))AA411 - 443240 - 272
21SERSERPHEPHE(chain B and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))BB173 - 3902 - 219
22THRTHRPHEPHE(chain B and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))BB392 - 409221 - 238
23METMETMETMET(chain B and (resid 173 through 390 or resid 392 through 409 or resid 411 through 443))BB411 - 443240 - 272

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Components

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


Mass: 31551.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASA1, GAP, RASA / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 3467.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NRY4
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.5 M Sodium Malonate pH 5.0, 0.1 M sodium acetate trihydrate salt, 6% PEG 20,000
Temp details: ambient 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→49.65 Å / Num. obs: 55390 / % possible obs: 100 % / Redundancy: 25.459 % / Biso Wilson estimate: 38.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.034 / Rrim(I) all: 0.17 / Χ2: 0.999 / Net I/av σ(I): 12.4 / Net I/σ(I): 12.37
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.95-2.0226.0292.331.9454920.70.4622.376
2.02-2.125.1071.5012.9753810.8370.3041.532
2.1-2.225.9091.1263.9257400.890.2251.149
2.2-2.3126.920.7755.851900.9440.1520.789
2.31-2.4626.1780.5877.4756510.9660.1160.598
2.46-2.6525.6720.4529.3455030.9780.0910.461
2.65-2.9125.4970.27913.8553950.9920.0570.285
2.91-3.3325.1010.17519.9155380.9960.0360.179
3.33-4.224.1430.11826.9456590.9970.0250.121
4.2-49.6524.1940.09129.9258410.9980.0190.093

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å82.16 Å
Translation1.95 Å82.16 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSB, 2J05

2gsb

2j05


Resolution: 1.95→49.65 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 2010 3.63 %
Rwork0.2135 53366 -
obs0.215 55376 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.99 Å2 / Biso mean: 50.6846 Å2 / Biso min: 20.05 Å2
Refinement stepCycle: final / Resolution: 1.95→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 21 233 5052
Biso mean--56.79 49.46 -
Num. residues----588
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2682X-RAY DIFFRACTION8.233TORSIONAL
12B2682X-RAY DIFFRACTION8.233TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-20.43791440.373537603904
2-2.050.3951390.322137653904
2.05-2.110.33981480.281137633911
2.11-2.180.3121410.271237523893
2.18-2.260.3121370.254537773914
2.26-2.350.26671350.24737733908
2.35-2.460.30531470.250537663913
2.46-2.590.30981440.251637963940
2.59-2.750.28221500.2438133963
2.75-2.960.29511330.22837883921
2.96-3.260.23711480.215938283976
3.26-3.730.24211430.186538403983
3.73-4.70.19311480.163938944042
4.7-49.650.23531530.199540514204
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)
15.9540.45770.49168.35430.69076.4947-0.01460.07760.05430.34830.0827-0.207-0.55180.2175-0.03620.3628-0.0495-0.0330.2961-0.0180.240925.46371.7593116.3373
23.36534.18752.48014.38572.79023.0424-0.07260.02890.42770.3191-0.13630.50930.129-0.18940.18310.33320.0148-0.04110.45310.01150.452214.625552.885690.1496
34.3841.73480.45983.88032.31894.4139-0.19890.89160.4533-0.23170.12550.2915-0.2735-0.31210.0310.289-0.0128-0.09230.45550.11610.378411.38448.146484.3965
45.1953-1.8246-0.00663.5835-0.92263.3454-0.007-0.0073-0.05230.00770.09960.1390.2093-0.0175-0.07980.2177-0.0045-0.06860.217-0.06240.248918.141543.6066108.3792
53.96150.2914-0.85786.9006-2.98058.4885-0.03730.08890.08330.13430.14840.1074-0.741-0.371-0.0940.36320.0022-0.03370.28440.0550.25929.319970.85671.014
63.4605-4.52483.28044.2987-3.51963.5398-0.07130.01050.5218-0.2199-0.181-0.7805-0.19880.22070.13290.4316-0.0002-0.05730.34090.00830.388240.080757.513693.4912
74.6554-2.69920.10693.6316-2.10176.2342-0.1744-0.67410.26660.14910.16010.1555-0.2380.10180.03570.2794-0.0204-0.09250.4995-0.06420.420544.660347.4353103.7576
85.67610.8325-1.0834.72271.12514.4346-0.0840.0558-0.31220.01070.1301-0.16740.4193-0.1459-0.05970.2512-0.0413-0.07360.280.03280.231738.101143.063679.0283
92.4861-3.4322-0.18356.81670.23338.69720.21940.73420.74221.0827-0.1164-0.5401-1.04030.1604-0.00190.5725-0.0499-0.04040.5713-0.06470.513627.720447.5822118.5579
107.6663-1.90531.34920.76981.19318.15170.1727-0.8453-0.17621.4586-0.0102-1.12090.57950.5221-0.02680.6339-0.133-0.11760.7169-0.00780.289131.780367.4462126.0922
114.38984.92110.11715.5934-0.25294.3705-0.0877-0.02-0.0846-1.01640.2134-0.6297-0.50890.56430.49760.4898-0.0940.0210.86470.09510.465136.97747.658768.2055
129.42353.1067-2.87049.6841.87794.4029-0.0929-0.6157-0.7011-0.182-0.77360.49860.1383-0.55150.35930.3017-0.1662-0.06890.9324-0.0340.380825.966840.325873.0716
139.0395-0.41992.48180.06790.49518.33820.27970.17320.0558-0.2997-0.3022-0.30410.8668-0.2742-0.10770.37850.0582-0.02030.52660.09270.291524.039367.29762.5328
141.05150.7239-0.08451.1307-1.10395.9572-0.0640.12160.50890.97060.64730.4798-1.0033-0.1465-0.61921.1219-0.03250.13461.0260.11080.454624.077681.435962.2573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 173 through 268 )A173 - 268
2X-RAY DIFFRACTION2chain 'A' and (resid 269 through 296 )A269 - 296
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 348 )A297 - 348
4X-RAY DIFFRACTION4chain 'A' and (resid 349 through 442 )A349 - 442
5X-RAY DIFFRACTION5chain 'B' and (resid 174 through 267 )B174 - 267
6X-RAY DIFFRACTION6chain 'B' and (resid 268 through 291 )B268 - 291
7X-RAY DIFFRACTION7chain 'B' and (resid 292 through 348 )B292 - 348
8X-RAY DIFFRACTION8chain 'B' and (resid 349 through 442 )B349 - 442
9X-RAY DIFFRACTION9chain 'U' and (resid 1085 through 1099 )U0
10X-RAY DIFFRACTION10chain 'U' and (resid 1100 through 1109 )U0
11X-RAY DIFFRACTION11chain 'V' and (resid 1084 through 1089 )V0
12X-RAY DIFFRACTION12chain 'V' and (resid 1090 through 1094 )V0
13X-RAY DIFFRACTION13chain 'V' and (resid 1103 through 1108 )V0
14X-RAY DIFFRACTION14chain 'V' and (resid 1109 through 1111 )V0

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