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- PDB-8atj: Crystal Structure of Shank2-SAM domain -

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Basic information

Entry
Database: PDB / ID: 8atj
TitleCrystal Structure of Shank2-SAM domain
ComponentsIsoform 4 of SH3 and multiple ankyrin repeat domains protein 2
KeywordsMETAL 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 / social behavior / associative learning / photoreceptor outer segment / synapse assembly / ionotropic glutamate receptor binding / hippocampal mossy fiber to CA3 synapse / photoreceptor inner segment / adult locomotory behavior / response to nutrient / learning / long-term synaptic potentiation / brush border membrane / brain development / SH3 domain binding / growth cone / dendritic spine / postsynaptic density / neuron projection / response to xenobiotic stimulus / apical plasma membrane / neuronal cell body / glutamatergic synapse / positive regulation of cell population proliferation / plasma membrane / cytosol
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. / Domain present in PSD-95, Dlg, and ZO-1/2. ...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. / SH3 domain
Similarity search - Domain/homology
FORMIC ACID / SH3 and multiple ankyrin repeat domains protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.117 Å
AuthorsBento, I. / Gracia Alai, M. / Kreienkamp, J.-H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Kr1321/9-1 Germany
CitationJournal: 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
DepositionAug 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Isoform 4 of SH3 and multiple ankyrin repeat domains protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2584
Polymers8,1111
Non-polymers1473
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-43 kcal/mol
Surface area4560 Å2
Unit cell
Length a, b, c (Å)57.490, 57.490, 48.033
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Isoform 4 of SH3 and multiple ankyrin repeat domains protein 2 / Shank2 / Cortactin-binding protein 1 / CortBP1 / Proline-rich synapse-associated protein 1


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
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis Tris pH5.5, 0.3M of Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F44

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
RfactorNum. reflection% reflection
Rfree0.2517 247 4.822 %
Rwork0.1956 4875 -
all0.198 --
obs-5122 98.085 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.269 Å20.135 Å20 Å2
2--0.269 Å2-0 Å2
3----0.873 Å2
Refinement stepCycle: LAST / Resolution: 2.117→49.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 0 5 51 626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013583
X-RAY DIFFRACTIONr_bond_other_d0.0010.017559
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.637787
X-RAY DIFFRACTIONr_angle_other_deg1.221.5981290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.684569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.58623.23534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62715109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.922154
X-RAY DIFFRACTIONr_chiral_restr0.0750.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02124
X-RAY DIFFRACTIONr_nbd_refined0.2140.2136
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.2522
X-RAY DIFFRACTIONr_nbtor_refined0.150.2273
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2490.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.26
X-RAY DIFFRACTIONr_nbd_other0.1250.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.27
X-RAY DIFFRACTIONr_mcbond_it2.6413.793279
X-RAY DIFFRACTIONr_mcbond_other2.643.792280
X-RAY DIFFRACTIONr_mcangle_it3.7745.662347
X-RAY DIFFRACTIONr_mcangle_other3.7695.68348
X-RAY DIFFRACTIONr_scbond_it3.5464.297304
X-RAY DIFFRACTIONr_scbond_other3.5214.305302
X-RAY DIFFRACTIONr_scangle_it5.4956.276440
X-RAY DIFFRACTIONr_scangle_other5.4976.272441
X-RAY DIFFRACTIONr_lrange_it7.99645.479665
X-RAY DIFFRACTIONr_lrange_other7.99645.153657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.117-2.1721.637131.3792671.3933780.4160.29474.07411.46
2.172-2.2310.328140.433530.4253670.6550.6261000.44
2.231-2.2960.339240.293460.2933700.7340.7951000.29
2.296-2.3660.271210.243280.2423490.8180.8461000.24
2.366-2.4440.246230.1953130.1983360.8590.8951000.191
2.444-2.5290.317140.2063300.213440.8740.8961000.205
2.529-2.6250.21160.213010.213170.9070.8851000.197
2.625-2.7320.20280.2422950.2413030.8170.8651000.227
2.732-2.8530.44990.2272930.2353020.8240.8721000.211
2.853-2.9910.19590.2132740.2132830.8950.8791000.2
2.991-3.1530.207130.1842520.1852650.8910.8991000.175
3.153-3.3430.376130.2062350.2142480.8520.9151000.189
3.343-3.5730.269140.1922370.1972510.9430.9461000.183
3.573-3.8570.38130.1442180.1472230.9260.96999.10310.136
3.857-4.2230.087100.1221900.122000.980.9781000.115
4.223-4.7170.168110.1121880.1151990.9630.9821000.107
4.717-5.4390.2160.141480.1461640.9650.971000.129
5.439-6.6410.2640.1831390.1851430.9560.9491000.174
6.641-9.3090.09890.1681060.1611150.9810.9621000.156
9.309-49.7880.68130.2620.219650.9950.9351000.182

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