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- PDB-3bxj: Crystal Structure of the C2-GAP Fragment of synGAP -

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Basic information

Entry
Database: PDB / ID: 3bxj
TitleCrystal Structure of the C2-GAP Fragment of synGAP
ComponentsRas GTPase-activating protein SynGAP
KeywordsSIGNALING PROTEIN / GTPase activating protein / GTPase activation / Membrane / Phosphoprotein / SH3-binding
Function / homology
Function and homology information


Regulation of RAS by GAPs / negative regulation of axonogenesis / pattern specification process / maintenance of postsynaptic specialization structure / negative regulation of Ras protein signal transduction / regulation of synapse structure or activity / dendrite development / receptor clustering / regulation of MAPK cascade / postsynaptic density, intracellular component ...Regulation of RAS by GAPs / negative regulation of axonogenesis / pattern specification process / maintenance of postsynaptic specialization structure / negative regulation of Ras protein signal transduction / regulation of synapse structure or activity / dendrite development / receptor clustering / regulation of MAPK cascade / postsynaptic density, intracellular component / axonogenesis / GTPase activator activity / dendritic shaft / regulation of long-term neuronal synaptic plasticity / visual learning / modulation of chemical synaptic transmission / regulation of synaptic plasticity / SH3 domain binding / neuron apoptotic process / negative regulation of neuron apoptotic process / Ras protein signal transduction / postsynaptic density / glutamatergic synapse / synapse / protein kinase binding / membrane / plasma membrane
Similarity search - Function
GTPase Activation - p120GAP; domain 1 - #20 / GTPase activation domain, GAP fold / p120GAP domain-like / Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site ...GTPase Activation - p120GAP; domain 1 - #20 / GTPase activation domain, GAP fold / p120GAP domain-like / Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Single Sheet / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ras/Rap GTPase-activating protein SynGAP
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsPena, V. / Hothorn, M. / Eberth, A. / Kaschau, N. / Parret, A. / Gremer, L. / Bonneau, F. / Ahmadian, M.R. / Scheffzek, K.
CitationJournal: Embo Rep. / Year: 2008
Title: The C2 domain of SynGAP is essential for stimulation of the Rap GTPase reaction.
Authors: Pena, V. / Hothorn, M. / Eberth, A. / Kaschau, N. / Parret, A. / Gremer, L. / Bonneau, F. / Ahmadian, M.R. / Scheffzek, K.
History
DepositionJan 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 SynGAP
B: Ras GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)108,8912
Polymers108,8912
Non-polymers00
Water00
1
A: Ras GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)54,4451
Polymers54,4451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)54,4451
Polymers54,4451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.320, 113.320, 166.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Ras GTPase-activating protein SynGAP / Synaptic Ras GTPase-activating protein 1 / Synaptic Ras-GAP 1 / Neuronal RasGAP / p135 SynGAP


Mass: 54445.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syngap1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9QUH6

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4.9
Details: 80 mM ammonium sulfate, 11% PEG 3000, 0.1 M sodium phosphate/citrate, 0.1mM EDTA as additive, pH 4.9, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→19.97 Å / Num. obs: 32876 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 57.974 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3-3.170.3835.1209123680100
3.17-40.13712.95865710312100
4-50.04333.2284384996100
5-60.03738.2126362229100
6-100.0344.7132612397100
10-120.02361.51485278100
12-140.0256075814999.3
14-160.01956.837479100
16-200.02455.33708197.6
20

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.579 / Cor.coef. Fo:Fc: 0.308
Highest resolutionLowest resolution
Translation3.5 Å12 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.97 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.891 / SU B: 28.18 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.516 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1644 5 %RANDOM
Rwork0.244 ---
obs0.246 32876 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.426 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å21.26 Å20 Å2
2--2.51 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 0 0 0 5491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225582
X-RAY DIFFRACTIONr_bond_other_d0.0010.023792
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9747531
X-RAY DIFFRACTIONr_angle_other_deg0.99339239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82824.073248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.71515991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7971538
X-RAY DIFFRACTIONr_chiral_restr0.0850.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026169
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021123
X-RAY DIFFRACTIONr_nbd_refined0.2450.21400
X-RAY DIFFRACTIONr_nbd_other0.1960.23864
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22723
X-RAY DIFFRACTIONr_nbtor_other0.0940.22992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.22
X-RAY DIFFRACTIONr_mcbond_it0.7771.54490
X-RAY DIFFRACTIONr_mcbond_other0.1021.51411
X-RAY DIFFRACTIONr_mcangle_it0.91825591
X-RAY DIFFRACTIONr_scbond_it1.53832366
X-RAY DIFFRACTIONr_scangle_it2.4154.51940
LS refinement shellResolution: 3→3.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 112 -
Rwork0.309 2129 -
all-2241 -
obs--100 %
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)
10.460.08491.49321.06170.02594.9071-0.0816-0.06240.32140.3274-0.04330.3054-0.4631-0.78080.12490.1077-0.00750.06330.00170.09950.07446.7327-11.52971.2121
21.37971.1838-0.91292.1793-1.61852.34720.0168-0.0126-0.0559-0.1868-0.0227-0.10790.05570.03170.0059-0.0456-0.03910.0002-0.1142-0.0389-0.119941.348-35.52716.2991
31.91622.2101-1.2343.5329-1.93432.2125-0.01870.0367-0.0348-0.1457-0.0749-0.17080.10290.01320.0935-0.15620.012-0.0453-0.098-0.0349-0.127144.7431-31.21356.301
40.01150.04720.41820.1941.717915.21590.0525-0.0652-0.15810.3583-0.0581-0.1816-0.21360.82150.00570.266-0.00720.01440.34540.05130.272986.9152-33.31936.5383
50.8043-0.9731-0.99341.89951.24032.1090.0703-0.0037-0.12740.1522-0.1340.13990.1269-0.23610.0637-0.0261-0.0172-0.0365-0.11660.0183-0.084560.0762-25.594831.7744
61.2448-0.7488-0.28412.08830.99262.10310.0383-0.0119-0.06750.1247-0.0529-0.02510.1302-0.09550.0145-0.0243-0.0692-0.01-0.20640.034-0.1259.0066-22.787330.9114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA238 - 4262 - 190
2X-RAY DIFFRACTION2AA427 - 565191 - 329
3X-RAY DIFFRACTION3AA566 - 713330 - 477
4X-RAY DIFFRACTION4BB237 - 4041 - 168
5X-RAY DIFFRACTION5BB405 - 525169 - 289
6X-RAY DIFFRACTION6BB526 - 719290 - 483

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