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- PDB-9ksq: Crystal Structure of the mouse Shank3 SAM domain -

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Basic information

Entry
Database: PDB / ID: 9ksq
TitleCrystal Structure of the mouse Shank3 SAM domain
ComponentsSH3 and multiple ankyrin repeat domains protein 3
KeywordsSTRUCTURAL PROTEIN / Self oligomerized domain
Function / homology
Function and homology information


response to interleukin-17 / regulation of AMPA glutamate receptor clustering / Neurexins and neuroligins / guanylate kinase-associated protein clustering / positive regulation of synapse structural plasticity / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / embryonic epithelial tube formation / regulation of grooming behavior ...response to interleukin-17 / regulation of AMPA glutamate receptor clustering / Neurexins and neuroligins / guanylate kinase-associated protein clustering / positive regulation of synapse structural plasticity / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / embryonic epithelial tube formation / regulation of grooming behavior / structural constituent of postsynaptic density / negative regulation of actin filament bundle assembly / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering / negative regulation of cell volume / RET signaling / vocalization behavior / neuron spine / AMPA glutamate receptor clustering / positive regulation of glutamate receptor signaling pathway / regulation of behavioral fear response / regulation of dendritic spine morphogenesis / dendritic spine morphogenesis / brain morphogenesis / locomotion / regulation of long-term synaptic potentiation / long-term synaptic depression / neural precursor cell proliferation / neuromuscular process controlling balance / ciliary membrane / positive regulation of dendritic spine development / exploration behavior / locomotory exploration behavior / associative learning / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / glial cell proliferation / synapse assembly / regulation of long-term synaptic depression / ionotropic glutamate receptor binding / positive regulation of long-term synaptic potentiation / learning / locomotory behavior / regulation of synaptic plasticity / modulation of chemical synaptic transmission / SH3 domain binding / memory / long-term synaptic potentiation / MAPK cascade / actin binding / scaffold protein binding / gene expression / dendritic spine / learning or memory / neuron projection / postsynaptic density / glutamatergic synapse / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. ...: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsZeyu, S. / Mingjie, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
CitationJournal: To Be Published
Title: Structure of Shank3 SAM domain at 2.79 Angstroms resolution
Authors: Shen, Z. / Zhang, M.
History
DepositionNov 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)9,5901
Polymers9,5901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.464, 63.464, 49.083
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2 / SPANK-2


Mass: 9589.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3, Kiaa1650, Prosap2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4ACU6
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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 2862 / % possible obs: 99.9 % / Redundancy: 10.25 % / Rrim(I) all: 0.289 / Net I/av σ(I): 6.94 / Net I/σ(I): 2.99
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 10.77 % / Mean I/σ(I) obs: 2.68 / Num. unique obs: 288 / Rrim(I) all: 0.833 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F3N

2f3n


Resolution: 2.79→31.73 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 143 5 %
Rwork0.201 --
obs0.2039 2862 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 0 601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01625
X-RAY DIFFRACTIONf_angle_d1.414843
X-RAY DIFFRACTIONf_dihedral_angle_d28.90181
X-RAY DIFFRACTIONf_chiral_restr0.0886
X-RAY DIFFRACTIONf_plane_restr0.009112
LS refinement shellResolution: 2.79→2.89 Å
RfactorNum. reflection% reflection
Rfree0.2546 143 -
Rwork0.201 2719 -
obs--100 %

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