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- PDB-5jxc: SynGAP Coiled-coil trimer -

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Basic information

Entry
Database: PDB / ID: 5jxc
TitleSynGAP Coiled-coil trimer
ComponentsRas/Rap GTPase-activating protein SynGAP
KeywordsSIGNALING PROTEIN / SynGAP / Coiled-Coil / Trimer
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 / regulation of GTPase activity / dendrite development / receptor clustering / regulation of MAPK cascade ...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 / regulation of GTPase activity / dendrite development / receptor clustering / regulation of MAPK cascade / postsynaptic density, intracellular component / GTPase activator activity / dendritic shaft / regulation of long-term neuronal synaptic plasticity / visual learning / regulation of synaptic plasticity / SH3 domain binding / negative regulation of neuron apoptotic process / Ras protein signal transduction / postsynaptic density / glutamatergic synapse / synapse / protein kinase binding / signal transduction / membrane / plasma membrane
Similarity search - Function
Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal 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 ...Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Ras/Rap GTPase-activating protein SynGAP / Ras/Rap GTPase-activating protein SynGAP
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsShang, Y. / Zhang, M.
Funding support Hong Kong, China, 5items
OrganizationGrant numberCountry
RGC663811 Hong Kong
RGC663812 Hong Kong
RGCT13-607/12R Hong Kong
RGCAoE-M09-12 Hong Kong
the Minister of Science and Technology of China2014CB910204 China
CitationJournal: Cell / Year: 2016
Title: Phase Transition in Postsynaptic Densities Underlies Formation of Synaptic Complexes and Synaptic Plasticity.
Authors: Zeng, M. / Shang, Y. / Araki, Y. / Guo, T. / Huganir, R.L. / Zhang, M.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras/Rap GTPase-activating protein SynGAP
B: Ras/Rap GTPase-activating protein SynGAP
C: Ras/Rap GTPase-activating protein SynGAP
D: Ras/Rap GTPase-activating protein SynGAP
E: Ras/Rap GTPase-activating protein SynGAP
F: Ras/Rap GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)67,4746
Polymers67,4746
Non-polymers00
Water64936
1
A: Ras/Rap GTPase-activating protein SynGAP
B: Ras/Rap GTPase-activating protein SynGAP
C: Ras/Rap GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)33,7373
Polymers33,7373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-63 kcal/mol
Surface area15120 Å2
MethodPISA
2
D: Ras/Rap GTPase-activating protein SynGAP
E: Ras/Rap GTPase-activating protein SynGAP
F: Ras/Rap GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)33,7373
Polymers33,7373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-63 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.803, 236.664, 42.207
Angle α, β, γ (deg.)90.00, 96.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ras/Rap GTPase-activating protein SynGAP


Mass: 11245.609 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1171-1258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syngap1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J9YUM2, UniProt: F6SEU4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES sodium pH 7.5, 0.1M L-proline, 20% w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97886 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19240 / % possible obs: 99.7 % / Redundancy: 3.8 % / Net I/σ(I): 22.8
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→39.497 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 36.45
RfactorNum. reflection% reflection
Rfree0.307 973 5.11 %
Rwork0.2229 --
obs0.2271 19058 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 0 36 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083825
X-RAY DIFFRACTIONf_angle_d0.9695122
X-RAY DIFFRACTIONf_dihedral_angle_d29.0761494
X-RAY DIFFRACTIONf_chiral_restr0.047593
X-RAY DIFFRACTIONf_plane_restr0.004669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.63190.36371460.29292543X-RAY DIFFRACTION97
2.6319-2.79680.3671130.28592591X-RAY DIFFRACTION99
2.7968-3.01270.36431420.2652579X-RAY DIFFRACTION99
3.0127-3.31570.44251620.28032549X-RAY DIFFRACTION100
3.3157-3.79520.31631430.21682608X-RAY DIFFRACTION100
3.7952-4.78020.24041260.18492663X-RAY DIFFRACTION100
4.7802-39.50140.27061410.2062552X-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)
12.46844.9799-0.32179.5379-0.06070.14950.126-0.14260.04010.2732-0.2466-0.02160.19180.02510.14940.6297-0.0253-0.00010.51110.06190.49580.3227-43.233444.2376
21.11952.41670.2184.38180.5007-0.09150.1240.1982-0.17151.13090.2208-0.28320.22240.0298-0.3650.7263-0.0567-0.07340.43210.07860.65326.1765-45.220544.4165
32.93225.02760.56888.60530.72640.1325-0.05830.11180.1766-0.0610.17810.08140.0759-0.0305-0.07080.5648-0.0562-0.03770.4296-0.00610.75251.9952-45.146437.9022
41.5017-2.08720.4484.5207-0.531-0.2483-0.4068-0.50030.18330.42320.5842-0.27720.1492-0.0744-0.2150.6030.11830.01120.4740.02310.41331.652336.158359.1523
53.8161-3.46570.65893.7898-0.47340.2664-0.2803-0.81740.5401-0.16340.624-0.65610.2196-0.112-0.21240.54640.11160.01920.5135-0.00740.3381-4.590137.205564.0582
65.117-5.98781.0056.399-0.94740.4698-0.0743-0.1765-0.23830.0350.17210.46450.1303-0.0109-0.03430.50770.01650.01990.47030.00420.449-4.300532.730958.1822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1189 through 1274 )
2X-RAY DIFFRACTION2chain B and (resid 1195 through 1272 )
3X-RAY DIFFRACTION3chain C and (resid 1194 through 1271 )
4X-RAY DIFFRACTION4chain D and (resid 1194 through 1271 )
5X-RAY DIFFRACTION5chain E and (resid 1189 through 1272 )
6X-RAY DIFFRACTION6chain F and (resid 1193 through 1272 )

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