+Open data
-Basic information
Entry | Database: PDB / ID: 8atj | ||||||
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Title | Crystal Structure of Shank2-SAM domain | ||||||
Components | Isoform 4 of SH3 and multiple ankyrin repeat domains protein 2 | ||||||
Keywords | METAL BINDING PROTEIN / synaptic scaffold protein / Zn2+ binding / Zn-dependent polymerization | ||||||
Function / homology | Function and homology information synaptic receptor adaptor activity / : / structural constituent of postsynaptic density / vocalization behavior / Neurexins and neuroligins / anchoring junction / long-term synaptic depression / ciliary membrane / adult behavior / regulation of synapse organization ...synaptic receptor adaptor activity / : / structural constituent of postsynaptic density / vocalization behavior / Neurexins and neuroligins / anchoring junction / long-term synaptic depression / ciliary membrane / adult behavior / regulation of synapse organization / negative regulation of hippo signaling / presynaptic active zone / associative learning / social behavior / photoreceptor outer segment / synapse assembly / hippocampal mossy fiber to CA3 synapse / photoreceptor inner segment / adult locomotory behavior / response to nutrient / learning / long-term synaptic potentiation / brush border membrane / ionotropic glutamate receptor binding / brain development / SH3 domain binding / growth cone / dendritic spine / postsynaptic density / response to xenobiotic stimulus / neuron projection / apical plasma membrane / neuronal cell body / glutamatergic synapse / positive regulation of cell population proliferation / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.117 Å | ||||||
Authors | Bento, I. / Gracia Alai, M. / Kreienkamp, J.-H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Mol Psychiatry / Year: 2022 Title: Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans. Authors: Hassani Nia, F. / Woike, D. / Bento, I. / Niebling, S. / Tibbe, D. / Schulz, K. / Hirnet, D. / Skiba, M. / Honck, H.H. / Veith, K. / Gunther, C. / Scholz, T. / Bierhals, T. / Driemeyer, J. / ...Authors: Hassani Nia, F. / Woike, D. / Bento, I. / Niebling, S. / Tibbe, D. / Schulz, K. / Hirnet, D. / Skiba, M. / Honck, H.H. / Veith, K. / Gunther, C. / Scholz, T. / Bierhals, T. / Driemeyer, J. / Bend, R. / Failla, A.V. / Lohr, C. / Alai, M.G. / Kreienkamp, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8atj.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8atj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8atj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8atj_validation.pdf.gz | 576.8 KB | Display | wwPDB validaton report |
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Full document | 8atj_full_validation.pdf.gz | 576.8 KB | Display | |
Data in XML | 8atj_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 8atj_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/8atj ftp://data.pdbj.org/pub/pdb/validation_reports/at/8atj | HTTPS FTP |
-Related structure data
Related structure data | 8b10C 2f44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8111.210 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 193T / Gene: SHANK2, CORTBP1, KIAA1022, PROSAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPX8 |
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#2: Chemical | ChemComp-FMT / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis Tris pH5.5, 0.3M of Magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.8 Å / Num. obs: 5201 / % possible obs: 99.92 % / Redundancy: 19.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2587 / Rpim(I) all: 0.05916 / Net I/σ(I): 10.07 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 516 / CC1/2: 0.568 / Rpim(I) all: 0.3268 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F44 Resolution: 2.117→49.788 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.048 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.196 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.747 Å2
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Refinement step | Cycle: LAST / Resolution: 2.117→49.788 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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