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- PDB-9bz4: Crystal structure of the C2 and GAP domains of human p120RasGAP -

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Basic information

Entry
Database: PDB / ID: 9bz4
TitleCrystal structure of the C2 and GAP domains of human p120RasGAP
ComponentsRas GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / Ras / C2 domain / GAP / RasGAP / RASA1
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 / mitotic cytokinesis / ephrin receptor signaling pathway / negative regulation of cell-matrix adhesion / 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 / mitotic cytokinesis / ephrin receptor signaling pathway / negative regulation of cell-matrix adhesion / 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 / regulation of cell shape / GTPase binding / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Ras GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPaul, M.E. / Boggon, T.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138411 United States
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)1R01GM102262 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32GM007324 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: The C2 domain augments Ras GTPase-activating protein catalytic activity.
Authors: Paul, M.E. / Chen, D. / Vish, K.J. / Lartey, N.L. / Hughes, E. / Freeman, Z.T. / Saunders, T.L. / Stiegler, A.L. / King, P.D. / Boggon, T.J.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: 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_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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
C: Ras GTPase-activating protein 1
D: Ras GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)214,2834
Polymers214,2834
Non-polymers00
Water46826
1
A: Ras GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)53,5711
Polymers53,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)53,5711
Polymers53,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)53,5711
Polymers53,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)53,5711
Polymers53,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.894, 94.036, 96.713
Angle α, β, γ (deg.)95.81, 111.10, 108.51
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 53570.703 Da / Num. of mol.: 4 / Fragment: UNP Residues 581-1047
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASA1, GAP, RASA / Plasmid: pET-32
Details (production host): modified to include TEV protease recognition sequence
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P20936
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M Ammonium Phosphate Dibasic 0.1M MOPS pH 7.4 26% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.44→87.52 Å / Num. obs: 75972 / % possible obs: 96.3 % / Redundancy: 10 % / CC1/2: 0.989 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.108 / Rrim(I) all: 0.34 / Net I/σ(I): 12.1
Reflection shellResolution: 2.45→2.57 Å / Redundancy: 7 % / Rmerge(I) obs: 1.495 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 10823 / CC1/2: 0.476 / Rpim(I) all: 0.641 / Rrim(I) all: 1.728 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
SCALA3.3.22data scaling
PHASER2.8.3phasing
XDS20220110data reduction
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→87.52 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 3884 5.12 %
Rwork0.2281 --
obs0.2309 71908 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.64 Å2
Refinement stepCycle: LAST / Resolution: 2.45→87.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14303 0 0 26 14329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314572
X-RAY DIFFRACTIONf_angle_d0.56219693
X-RAY DIFFRACTIONf_dihedral_angle_d4.8599023
X-RAY DIFFRACTIONf_chiral_restr0.0372297
X-RAY DIFFRACTIONf_plane_restr0.0052491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.470.43031220.35032102X-RAY DIFFRACTION79
2.47-2.510.36021190.3282444X-RAY DIFFRACTION90
2.51-2.540.37771250.32192472X-RAY DIFFRACTION91
2.54-2.570.35381270.30152567X-RAY DIFFRACTION97
2.57-2.610.32561510.29132631X-RAY DIFFRACTION97
2.61-2.650.35671430.29982607X-RAY DIFFRACTION97
2.65-2.690.36411640.28232645X-RAY DIFFRACTION98
2.69-2.740.33831490.27372579X-RAY DIFFRACTION97
2.74-2.780.38061550.27632584X-RAY DIFFRACTION98
2.78-2.830.31441230.26852669X-RAY DIFFRACTION97
2.83-2.890.31911210.26722591X-RAY DIFFRACTION98
2.89-2.950.32321530.26872655X-RAY DIFFRACTION97
2.95-3.010.33281520.28522548X-RAY DIFFRACTION97
3.01-3.080.31341380.28982639X-RAY DIFFRACTION97
3.08-3.160.33121530.28342571X-RAY DIFFRACTION97
3.16-3.240.33321270.27342651X-RAY DIFFRACTION97
3.24-3.340.29931470.25172567X-RAY DIFFRACTION96
3.34-3.450.27991460.22662564X-RAY DIFFRACTION96
3.45-3.570.3111460.22392532X-RAY DIFFRACTION94
3.57-3.710.27131400.22742422X-RAY DIFFRACTION91
3.71-3.880.29291700.22022619X-RAY DIFFRACTION98
3.88-4.090.26431320.20142657X-RAY DIFFRACTION98
4.09-4.340.27751130.19152651X-RAY DIFFRACTION98
4.34-4.680.25071120.1862645X-RAY DIFFRACTION98
4.68-5.150.26071360.18712625X-RAY DIFFRACTION97
5.15-5.890.31161330.21482595X-RAY DIFFRACTION96
5.89-7.420.30671230.25582471X-RAY DIFFRACTION92
7.42-87.520.21640.19932605X-RAY DIFFRACTION98
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)
13.414-2.56280.04517.51091.21062.471-0.0433-0.03210.1983-0.01050.2320.1284-0.0865-0.2862-0.1310.3223-0.00520.02390.59550.02680.394920.854420.348850.1349
21.9067-1.2731.30382.1257-2.36324.5023-0.2660.26190.27090.1916-0.1198-0.1821-0.47510.30230.34650.3951-0.1378-0.03210.43080.0370.456722.56.933214.2495
32.20490.31520.51092.8079-2.16636.18460.0959-0.22530.0307-0.0567-0.20420.01160.17190.04610.07850.4030.03910.01090.3437-0.04290.408624.4309-13.142337.8059
45.41243.50652.19866.89322.51443.28580.00280.3344-0.4658-0.12730.2331-0.12210.39620.385-0.28880.32620.1209-0.00090.5331-0.01750.456129.3243-37.817455.6948
50.76570.19550.06432.72242.25285.8984-0.10160.0623-0.13570.0381-0.00330.06650.73910.3753-0.05120.41420.07020.00140.57970.07470.578363.0252-28.844155.0059
61.441-0.1625-1.5861.99190.89364.4229-0.05220.113-0.0721-0.38540.10520.07470.4513-0.2757-0.10940.4979-0.0327-0.12710.44620.08180.488566.5004-31.506649.4084
72.82833.62640.26978.38061.81172.7622-0.1546-0.0932-0.12440.19130.0980.11560.05170.1740.0950.31470.10030.00510.51820.04440.327120.4048-25.849576.3911
83.9184-0.616-0.32125.7495-2.55648.9556-0.2573-0.248-0.00170.20530.17740.1773-0.4072-0.41320.00090.40510.0074-0.08860.41590.01840.367423.63641.286298.8958
93.34322.657-1.20457.6793-2.46014.1475-0.1970.0934-0.599-0.3881-0.106-0.51980.44920.12990.28790.40330.0541-0.00090.5243-0.030.418223.843-20.6362117.9973
100.84390.2818-0.7812.0367-3.06845.4225-0.24460.05530.0751-0.2175-0.0447-0.24630.0189-0.06770.2920.5270.0128-0.07610.3775-0.04890.457422.6992-0.088799.7516
115.0959-4.4436-3.92897.92363.82366.06340.4732-0.20340.66560.05670.1565-0.168-0.89620.2411-0.70940.5167-0.1010.12980.5896-0.06250.606830.02131.738471.4179
127.4252.14713.04554.27861.70996.96610.1122-0.20560.29320.0078-0.284-0.0919-0.4277-0.17270.21680.4220.04130.03220.490.01860.334763.942820.093864.6752
133.8327-1.1479-2.26227.09674.44438.4230.0351-0.20190.32470.8141-0.04360.3219-0.0137-0.9230.07670.57430.00730.01720.67580.09230.401765.202628.634189.484
141.50030.00751.7131.37471.27376.3409-0.0884-0.04750.12550.1668-0.13930.1133-0.1348-0.2230.18030.32870.02730.03770.39470.03550.478663.697523.409470.1685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 588 through 717 )
2X-RAY DIFFRACTION2chain 'B' and (resid 718 through 974 )
3X-RAY DIFFRACTION3chain 'B' and (resid 975 through 1044 )
4X-RAY DIFFRACTION4chain 'C' and (resid 588 through 717 )
5X-RAY DIFFRACTION5chain 'C' and (resid 718 through 840 )
6X-RAY DIFFRACTION6chain 'C' and (resid 841 through 1043 )
7X-RAY DIFFRACTION7chain 'A' and (resid 588 through 717 )
8X-RAY DIFFRACTION8chain 'A' and (resid 718 through 806 )
9X-RAY DIFFRACTION9chain 'A' and (resid 807 through 947 )
10X-RAY DIFFRACTION10chain 'A' and (resid 948 through 1044 )
11X-RAY DIFFRACTION11chain 'D' and (resid 588 through 717 )
12X-RAY DIFFRACTION12chain 'D' and (resid 718 through 806 )
13X-RAY DIFFRACTION13chain 'D' and (resid 807 through 925 )
14X-RAY DIFFRACTION14chain 'D' and (resid 926 through 1043 )

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