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- PDB-8ym2: Crystal structure of AIDA-1 PTB domain in complex with SynGAP NPx... -

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Basic information

Entry
Database: PDB / ID: 8ym2
TitleCrystal structure of AIDA-1 PTB domain in complex with SynGAP NPxF motif
Components
  • Ankyrin repeat and sterile alpha motif domain-containing protein 1B
  • Ras/Rap GTPase-activating protein SynGAP
KeywordsPROTEIN BINDING / AIDA-1 / ANKS1B / SynGAP / Ras and Rab interactor / PTB domain
Function / homology
Function and homology information


Regulation of RAS by GAPs / negative regulation of axonogenesis / maintenance of postsynaptic specialization structure / pattern specification process / negative regulation of Ras protein signal transduction / regulation of synapse structure or activity / receptor clustering / dendrite development / regulation of MAPK cascade / ephrin receptor signaling pathway ...Regulation of RAS by GAPs / negative regulation of axonogenesis / maintenance of postsynaptic specialization structure / pattern specification process / negative regulation of Ras protein signal transduction / regulation of synapse structure or activity / receptor clustering / dendrite development / regulation of MAPK cascade / ephrin receptor signaling pathway / postsynaptic density, intracellular component / ephrin receptor binding / GTPase activator activity / axonogenesis / dendritic shaft / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / visual learning / regulation of synaptic plasticity / SH3 domain binding / neuron apoptotic process / negative regulation of neuron apoptotic process / Ras protein signal transduction / postsynaptic density / synapse / protein kinase binding / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal domain / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase ...Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal domain / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / 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 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SAM domain (Sterile alpha motif) / Rho GTPase activation protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Ankyrin repeat and sterile alpha motif domain-containing protein 1B / Ras/Rap GTPase-activating protein SynGAP
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, X. / Wang, Y. / Cai, Q. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508402 China
CitationJournal: J.Mol.Biol. / Year: 2024
Title: AIDA-1/ANKS1B Binds to the SynGAP Family RasGAPs with High Affinity and Specificity.
Authors: Wang, X. / Wang, Y. / Cai, Q. / Zhang, M.
History
DepositionMar 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat and sterile alpha motif domain-containing protein 1B
B: Ras/Rap GTPase-activating protein SynGAP


Theoretical massNumber of molelcules
Total (without water)19,5802
Polymers19,5802
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-13 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.919, 112.919, 112.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Ankyrin repeat and sterile alpha motif domain-containing protein 1B


Mass: 18248.781 Da / Num. of mol.: 1 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anks1b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BZM2
#2: Protein/peptide Ras/Rap GTPase-activating protein SynGAP / Neuronal RasGAP / Synaptic Ras GTPase-activating protein 1 / Synaptic Ras-GAP 1 / p135 SynGAP


Mass: 1331.560 Da / Num. of mol.: 1 / Fragment: NPxF motif / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q9QUH6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.1
Details: 1.8 M (NH4)2SO4, 10% 1,4-Dioxane, and 0.1 M MES at pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16295 / % possible obs: 100 % / Redundancy: 39 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.03 / Rrim(I) all: 0.178 / Χ2: 1.173 / Net I/σ(I): 3.1 / Num. measured all: 635160
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2-2.0340.62.5178080.6970.9060.3992.5480.426
2.03-2.0740.51.8438110.6960.9060.2931.8660.439
2.07-2.1140.41.6457820.7950.9410.2611.6650.432
2.11-2.1540.61.5878130.840.9560.2521.6070.438
2.15-2.240.38020.8630.9631.7590.671
2.2-2.2534.83.0558150.9510.9870.5183.0991.826
2.25-2.3136.85.2178040.9560.9890.8725.2911.846
2.31-2.3735.81.1598080.9460.9860.1961.1750.568
2.37-2.4437.80.6968120.9640.9910.1140.7060.519
2.44-2.5241.70.5668040.980.9950.0890.5730.556
2.52-2.6142.10.4828050.9860.9960.0750.4880.594
2.61-2.7141.70.3638240.9930.9980.0570.3680.704
2.71-2.8441.20.3198000.9920.9980.050.3230.786
2.84-2.9940.80.2568060.9950.9990.0410.260.954
2.99-3.1739.60.2038200.9950.9990.0330.2061.243
3.17-3.4235.40.1718240.9960.9990.0290.1741.673
3.42-3.7636.90.1548270.99810.0260.1562.683
3.76-4.3139.80.1198270.99810.0190.1212.704
4.31-5.4337.90.1048320.99910.0170.1062.586
5.43-5035.30.0928710.99910.0160.0942.159

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ITU

6itu


Resolution: 2→25.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.198 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26378 750 4.7 %RANDOM
Rwork0.21311 ---
obs0.21551 15191 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.826 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 30 1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121292
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161173
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6511744
X-RAY DIFFRACTIONr_angle_other_deg0.4831.5722741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.55353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22110223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.745.449629
X-RAY DIFFRACTIONr_mcbond_other4.7355.449629
X-RAY DIFFRACTIONr_mcangle_it6.6018.088778
X-RAY DIFFRACTIONr_mcangle_other6.5978.089779
X-RAY DIFFRACTIONr_scbond_it5.7095.991663
X-RAY DIFFRACTIONr_scbond_other5.7065.991664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2658.725966
X-RAY DIFFRACTIONr_long_range_B_refined12.448108.3245210
X-RAY DIFFRACTIONr_long_range_B_other12.433108.145203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 56 -
Rwork0.293 1143 -
obs--100 %

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