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- PDB-6wax: C-terminal SH2 domain of p120RasGAP -

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Basic information

Entry
Database: PDB / ID: 6wax
TitleC-terminal SH2 domain of p120RasGAP
ComponentsRas GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / SH2 domain / RasGAP / phosphopeptide / phosphotyrosine
Function / homology
Function and homology information


regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / blood vessel morphogenesis / negative regulation of cell-matrix adhesion / mitotic cytokinesis / ephrin receptor signaling pathway / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases ...regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / blood vessel morphogenesis / negative regulation of cell-matrix adhesion / mitotic cytokinesis / ephrin receptor signaling pathway / vasculogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ruffle / EPHB-mediated forward signaling / phosphotyrosine residue binding / Downstream signal transduction / GTPase activator activity / VEGFR2 mediated cell proliferation / Regulation of RAS by GAPs / GTPase binding / regulation of cell shape / negative regulation of neuron apoptotic process / intracellular signal transduction / signaling receptor binding / GTPase activity / negative regulation of apoptotic process / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / 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 ...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 / 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 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ras GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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

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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
B: Ras GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,50010
Polymers24,9362
Non-polymers5658
Water4,378243
1
A: Ras GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7505
Polymers12,4681
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7505
Polymers12,4681
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.499, 65.588, 71.614
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 343 through 395 or resid 397...
21(chain B and (resid 343 through 395 or resid 397...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 343 through 395 or resid 397...A343 - 395
121(chain A and (resid 343 through 395 or resid 397...A397 - 401
131(chain A and (resid 343 through 395 or resid 397...A403 - 409
141(chain A and (resid 343 through 395 or resid 397...A412 - 413
151(chain A and (resid 343 through 395 or resid 397...A415 - 422
161(chain A and (resid 343 through 395 or resid 397...A425 - 431
171(chain A and (resid 343 through 395 or resid 397...A433 - 444
211(chain B and (resid 343 through 395 or resid 397...B343 - 395
221(chain B and (resid 343 through 395 or resid 397...B397 - 401
231(chain B and (resid 343 through 395 or resid 397...B343 - 444
241(chain B and (resid 343 through 395 or resid 397...B425 - 43
251(chain B and (resid 343 through 395 or resid 397...B425 - 431
261(chain B and (resid 343 through 395 or resid 397...B433 - 444

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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.: 2 / 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.3 M Ammonium Sulfate, 0.1 M Bis Tris pH 6.5 / 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: 0.9792 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: 1.5→50 Å / Num. obs: 40194 / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.028 / Rrim(I) all: 0.099 / Χ2: 1.002 / Net I/σ(I): 7.4 / Num. measured all: 471661
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5571.02639410.6890.4071.1060.99899.9
1.55-1.629.40.80839590.8460.2670.8530.996100
1.62-1.6912.30.61339730.9180.1770.6380.997100
1.69-1.7812.70.43239610.9620.1240.450.998100
1.78-1.8912.40.29539890.9820.0860.3070.993100
1.89-2.0412.40.20239780.9880.0590.211.01299.9
2.04-2.2412.90.15640140.9910.0440.1620.99199.9
2.24-2.5613.10.12540240.9940.0350.130.99399.8
2.56-3.2312.50.09540850.9960.0270.0991.043100
3.23-5012.50.07342700.9970.0210.0760.998100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D4T

1d4t


Resolution: 1.5→48.368 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.1968 1943 4.84 %
Rwork0.1791 --
obs0.1799 40121 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.38 Å2 / Biso mean: 32.8258 Å2 / Biso min: 17.78 Å2
Refinement stepCycle: final / Resolution: 1.5→48.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 34 243 1991
Biso mean--48.87 42.29 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061882
X-RAY DIFFRACTIONf_angle_d0.8722544
X-RAY DIFFRACTIONf_dihedral_angle_d12.2971126
X-RAY DIFFRACTIONf_chiral_restr0.06248
X-RAY DIFFRACTIONf_plane_restr0.007340
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A874X-RAY DIFFRACTION8.306TORSIONAL
12B874X-RAY DIFFRACTION8.306TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5004-1.53790.29691260.2847259095
1.5379-1.57950.28091440.2532662100
1.5795-1.6260.27151460.23592711100
1.626-1.67850.25681270.22222704100
1.6785-1.73850.26961460.21732689100
1.7385-1.80810.22891650.20312682100
1.8081-1.89040.23481430.20082707100
1.8904-1.990.22671510.18822715100
1.99-2.11470.22631450.18592718100
2.1147-2.2780.22641420.17542732100
2.278-2.50720.20081240.17362743100
2.5072-2.870.20771320.18382763100
2.87-3.61570.18321120.17062822100
3.6157-48.3680.15271400.1622940100
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)
14.8606-3.346-4.98383.37611.94447.1828-0.4963-0.6289-0.04420.6560.40420.22840.18040.08130.06180.27280.02190.01770.28740.00170.3033-0.431855.367359.5254
26.33052.67591.34657.9741-1.19675.09210.1051-0.8328-0.13660.2654-0.1430.02320.2406-0.1883-0.0060.16030.01160.01850.25620.0040.16459.49453.96458.6446
34.64790.7588-0.6543.40122.03055.33340.0018-0.17690.1525-0.01550.0175-0.3130.12510.37120.02270.21380.0193-0.02240.28010.01250.252220.946153.109757.6397
46.5553-4.5241-1.89046.26551.40294.7436-0.1259-0.29420.63830.24630.1887-0.314-0.20010.2052-0.13050.1461-0.02-0.02360.1777-0.03520.20212.295360.861854.3683
54.2804-5.77834.09749.026-4.17475.5375-0.2096-0.04811.00530.1612-0.1408-0.8516-0.25120.65790.18780.2167-0.0582-0.00940.2517-0.01810.273218.978161.038349.5511
63.8822-3.9939-2.73914.25923.86788.4924-0.127-0.5288-0.08760.0647-0.04260.2705-0.2720.00220.19250.25980.01980.00260.20570.02380.26072.605964.338545.2175
78.1325.87120.48898.8603-2.05157.998-0.09150.29460.1087-0.62230.150.14070.00880.2-0.10870.25530.0093-0.00590.2221-0.00350.25475.031561.918240.3535
88.5255-5.6102-5.02697.9125-0.57428.6367-0.19520.3531-0.0711-0.2620.057-0.02360.1992-0.09250.11180.2177-0.0297-0.03580.1899-0.00720.20449.746253.264841.9622
95.75034.1849-0.43793.9091-0.69862.2203-0.42161.43040.5605-0.9630.0708-0.3876-0.50521.51150.23210.367-0.0580.04710.45560.12510.368520.412956.905438.9193
102.48992.2799-0.63758.8528-3.41226.94440.1083-0.1479-0.19060.4561-0.04680.04030.217-0.2931-0.23980.22130.00860.02160.27710.02570.279616.737449.316849.7797
112.7831-2.77530.02233.98842.45866.0883-0.004-1.1315-1.44281.23331.1343-3.41841.19821.4784-1.09520.54940.0442-0.18770.6891-0.20041.175426.661535.461952.056
127.05052.2559-1.08066.013-0.83743.92760.314-0.248-0.12920.4797-0.2250.1291-0.05930.025-0.09110.2521-0.01630.01510.17580.01140.164610.327933.403851.4244
138.8109-6.8736-2.3849.67370.50133.79860.25410.346-0.8329-0.2549-0.05060.55790.1394-0.3-0.22460.2215-0.0639-0.02990.19970.0310.265811.266728.849643.6711
145.9045-1.1824-2.70392.90150.53892.32340.16660.2150.0916-0.1233-0.0157-0.0226-0.1369-0.0343-0.13630.2231-0.0178-0.0040.18820.00840.172518.178436.427239.4284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 340 through 349 )A340 - 349
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 357 )A350 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 373 )A358 - 373
4X-RAY DIFFRACTION4chain 'A' and (resid 374 through 391 )A374 - 391
5X-RAY DIFFRACTION5chain 'A' and (resid 392 through 402 )A392 - 402
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 411 )A403 - 411
7X-RAY DIFFRACTION7chain 'A' and (resid 412 through 418 )A412 - 418
8X-RAY DIFFRACTION8chain 'A' and (resid 419 through 428 )A419 - 428
9X-RAY DIFFRACTION9chain 'A' and (resid 429 through 433 )A429 - 433
10X-RAY DIFFRACTION10chain 'A' and (resid 434 through 444 )A434 - 444
11X-RAY DIFFRACTION11chain 'B' and (resid 343 through 348 )B343 - 348
12X-RAY DIFFRACTION12chain 'B' and (resid 349 through 378 )B349 - 378
13X-RAY DIFFRACTION13chain 'B' and (resid 379 through 401 )B379 - 401
14X-RAY DIFFRACTION14chain 'B' and (resid 402 through 444 )B402 - 444

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