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- PDB-2f3n: Crystal Structure of the native Shank SAM domain. -

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Basic information

Entry
Database: PDB / ID: 2f3n
TitleCrystal Structure of the native Shank SAM domain.
ComponentsSH3 and multiple ankyrin repeat domains 3
KeywordsSTRUCTURAL PROTEIN / Postsynaptic density / SAM domain / shank / scaffolding protein
Function / homology
Function and homology information


response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation ...response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation / NMDA glutamate receptor clustering / Neurexins and neuroligins / positive regulation of synapse structural plasticity / negative regulation of actin filament bundle assembly / vocal learning / negative regulation of cell volume / regulation of behavioral fear response / positive regulation of long-term neuronal synaptic plasticity / regulation of grooming behavior / structural constituent of postsynaptic density / AMPA glutamate receptor clustering / vocalization behavior / neuron spine / regulation of dendritic spine morphogenesis / neural precursor cell proliferation / locomotion / dendritic spine morphogenesis / brain morphogenesis / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / regulation of postsynapse organization / positive regulation of dendritic spine development / exploration behavior / ciliary membrane / regulation of long-term synaptic depression / adult behavior / locomotory exploration behavior / postsynaptic density, intracellular component / social behavior / positive regulation of excitatory postsynaptic potential / associative learning / neuromuscular process controlling balance / glial cell proliferation / synapse assembly / ionotropic glutamate receptor binding / positive regulation of synaptic transmission, glutamatergic / locomotory behavior / learning / long-term synaptic potentiation / G protein-coupled receptor binding / positive regulation of long-term synaptic potentiation / regulation of synaptic plasticity / modulation of chemical synaptic transmission / memory / SH3 domain binding / : / MAPK cascade / gene expression / actin binding / scaffold protein binding / dendritic spine / postsynaptic density / learning or memory / neuron projection / glutamatergic synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Transcription Factor, Ets-1 / 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. ...Transcription Factor, Ets-1 / 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 / Ankyrin repeats (3 copies) / PDZ superfamily / 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. / DNA polymerase; domain 1 / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, MAD / Resolution: 2.1 Å
AuthorsBaron, M.K. / Bowie, J.U. / Faham, S.
CitationJournal: Science / Year: 2006
Title: An architectural framework that may lie at the core of the postsynaptic density.
Authors: Baron, M.K. / Boeckers, T.M. / Vaida, B. / Faham, S. / Gingery, M. / Sawaya, M.R. / Salyer, D. / Gundelfinger, E.D. / Bowie, J.U.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains 3
B: SH3 and multiple ankyrin repeat domains 3
C: SH3 and multiple ankyrin repeat domains 3


Theoretical massNumber of molelcules
Total (without water)27,2763
Polymers27,2763
Non-polymers00
Water2,918162
1
A: SH3 and multiple ankyrin repeat domains 3


Theoretical massNumber of molelcules
Total (without water)9,0921
Polymers9,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains 3


Theoretical massNumber of molelcules
Total (without water)9,0921
Polymers9,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SH3 and multiple ankyrin repeat domains 3


Theoretical massNumber of molelcules
Total (without water)9,0921
Polymers9,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.715, 104.715, 40.188
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 3 / Shank3 / Proline-rich synapse associated protein 2 / ProSAP2 / SPANK-2


Mass: 9092.104 Da / Num. of mol.: 3 / Fragment: SAM Domain / Mutation: M55E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank3 / Plasmid: Pet3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9JLU4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Well solution: 0.1 M HEPES pH 7.2, 0.4M Ammonium Formate, 6.5 mM N-nonyl BD Glucoside. Protein Buffer: 5mM tris pH 8.0, 50 mM NaCl, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277.K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 14919 / Num. obs: 14919 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.087 / Net I/σ(I): 34.6
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 9.6 / Rsym value: 0.364 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: SIR, MAD / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 728 -RANDOM
Rwork0.206 ---
all0.208 14682 --
obs0.206 14682 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 0 162 1755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39611
X-RAY DIFFRACTIONc_bond_d0.010305

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