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- PDB-2awu: Synapse associated protein 97 PDZ2 domain variant C378G -

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Basic information

Entry
Database: PDB / ID: 2awu
TitleSynapse associated protein 97 PDZ2 domain variant C378G
Components
  • AHH
  • Synapse-associated protein 97
KeywordsMEMBRANE PROTEIN / synaptic signaling / trafficking protein
Function / homology
Function and homology information


tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / cortical microtubule organization ...tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / cell projection membrane / paranode region of axon / smooth muscle tissue development / bicellular tight junction assembly / Trafficking of AMPA receptors / positive regulation of potassium ion transport / amyloid precursor protein metabolic process / Activation of Ca-permeable Kainate Receptor / regulation of ventricular cardiac muscle cell action potential / node of Ranvier / establishment or maintenance of epithelial cell apical/basal polarity / protein-containing complex localization / endothelial cell proliferation / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / ureteric bud development / regulation of myelination / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / postsynaptic density, intracellular component / microvillus / kinesin binding / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / potassium channel regulator activity / lateral plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / ionotropic glutamate receptor binding / T-tubule / actin filament polymerization / regulation of membrane potential / T cell activation / basal plasma membrane / synaptic membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / actin filament organization / PDZ domain binding / protein localization to plasma membrane / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / neuromuscular junction / protein localization / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / synaptic vesicle membrane / cell-cell adhesion / cerebral cortex development / regulation of protein localization / negative regulation of epithelial cell proliferation / cell-cell junction / presynaptic membrane / cell junction / regulation of cell shape / chemical synaptic transmission / postsynaptic membrane / basolateral plasma membrane / cell population proliferation / microtubule / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / cell adhesion / neuron projection / membrane raft / apical plasma membrane / dendrite / neuronal cell body / glutamatergic synapse / synapse / positive regulation of cell population proliferation
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / Polyubiquitination (PEST) N-terminal domain of MAGUK / L27 domain superfamily / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / Polyubiquitination (PEST) N-terminal domain of MAGUK / L27 domain superfamily / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsVon Ossowski, I. / Oksanen, E. / Von Ossowski, L. / Cai, C. / Sundberg, M. / Goldman, A. / Keinanen, K.
CitationJournal: Febs J. / Year: 2006
Title: Crystal structure of the second PDZ domain of SAP97 in complex with a GluR-A C-terminal peptide
Authors: von Ossowski, I. / Oksanen, E. / von Ossowski, L. / Cai, C. / Sundberg, M. / Goldman, A. / Keinanen, K.
History
DepositionSep 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synapse-associated protein 97
B: Synapse-associated protein 97
C: AHH


Theoretical massNumber of molelcules
Total (without water)23,2163
Polymers23,2163
Non-polymers00
Water1,33374
1
A: Synapse-associated protein 97


Theoretical massNumber of molelcules
Total (without water)11,4251
Polymers11,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Synapse-associated protein 97


Theoretical massNumber of molelcules
Total (without water)11,4251
Polymers11,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AHH


  • defined by author
  • 365 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3651
Polymers3651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.220, 52.140, 52.640
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Synapse-associated protein 97 / Presynaptic protein SAP97 / SAP-97


Mass: 11425.163 Da / Num. of mol.: 2 / Fragment: PDZ2 domain / Mutation: C378G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg1 / Plasmid: PK0302-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q62696
#2: Protein/peptide AHH


Mass: 365.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the peptide was chemicaly synthesized
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.9 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate, 0.1M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.519 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 11, 2005
RadiationMonochromator: Double crystal silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.519 Å / Relative weight: 1
ReflectionResolution: 2.44→20 Å / Num. all: 6219 / Num. obs: 6219 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.029 / Net I/σ(I): 37.19
Reflection shellResolution: 2.44→2.59 Å / % possible obs: 90.8 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 17.84 / Num. measured obs: 6332 / Num. unique obs: 1766 / % possible all: 91.6

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Phasing

Phasing MRRfactor: 0.436 / Cor.coef. Fo:Fc: 0.544
Highest resolutionLowest resolution
Rotation3 Å19.65 Å
Translation3 Å19.65 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→19.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.848 / SU B: 10.267 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.822 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 311 5 %RANDOM
Rwork0.18 ---
all0.186 6219 --
obs0.186 6219 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.63 Å2
2---0.33 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.44→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 74 1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221401
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9731891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30826.53149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38115246
X-RAY DIFFRACTIONr_chiral_restr0.10.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021012
X-RAY DIFFRACTIONr_nbd_refined0.220.2563
X-RAY DIFFRACTIONr_nbtor_refined0.310.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.28
X-RAY DIFFRACTIONr_mcbond_it0.821.5942
X-RAY DIFFRACTIONr_mcangle_it1.42621469
X-RAY DIFFRACTIONr_scbond_it2.113504
X-RAY DIFFRACTIONr_scangle_it3.2124.5422
LS refinement shellResolution: 2.442→2.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 20 -
Rwork0.209 396 -
all-416 -
obs--100 %

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