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- PDB-2aww: Synapse associated protein 97 PDZ2 domain variant C378G with C-te... -

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Basic information

Entry
Database: PDB / ID: 2aww
TitleSynapse associated protein 97 PDZ2 domain variant C378G with C-terminal GluR-A peptide
Components
  • 18-residue C-terminal peptide from glutamate receptor, ionotropic, AMPA1
  • 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 / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine ...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 / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / hard palate development / COPII-mediated vesicle transport / positive regulation of membrane potential / establishment of centrosome localization / negative regulation of p38MAPK cascade / cortical microtubule organization / embryonic skeletal system morphogenesis / astral microtubule organization / cellular response to ammonium ion / structural constituent of postsynaptic density / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath abaxonal region / receptor localization to synapse / peristalsis / cell projection membrane / smooth muscle tissue development / paranode region of axon / myosin V binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / bicellular tight junction assembly / positive regulation of potassium ion transport / Trafficking of AMPA receptors / neuron spine / Activation of Ca-permeable Kainate Receptor / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / response to arsenic-containing substance / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to dsRNA / dendritic spine membrane / amyloid precursor protein metabolic process / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / long-term synaptic depression / lens development in camera-type eye / endothelial cell proliferation / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / ureteric bud development / regulation of myelination / neurotransmitter receptor localization to postsynaptic specialization membrane / protein kinase A binding / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / positive regulation of actin filament polymerization / neuronal cell body membrane / Activation of AMPA receptors / receptor clustering / perisynaptic space / AMPA glutamate receptor activity / kinesin binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / regulation of postsynaptic membrane neurotransmitter receptor levels / immunoglobulin binding / microvillus / AMPA glutamate receptor complex / adenylate cyclase binding / cellular response to organic cyclic compound / ionotropic glutamate receptor complex / immunological synapse / excitatory synapse / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuronal action potential / basement membrane / lateral plasma membrane / asymmetric synapse / G-protein alpha-subunit binding / regulation of receptor recycling / potassium channel regulator activity / bicellular tight junction / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / postsynaptic density, intracellular component / positive regulation of synaptic transmission / glutamate receptor binding / long-term memory / negative regulation of T cell proliferation / T cell proliferation / response to electrical stimulus / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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 / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Periplasmic binding protein-like I / 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
: / Glutamate receptor 1 / Disks large homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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: 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 1.5May 29, 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: Synapse associated protein 97
B: Synapse associated protein 97
C: 18-residue C-terminal peptide from glutamate receptor, ionotropic, AMPA1


Theoretical massNumber of molelcules
Total (without water)24,4853
Polymers24,4853
Non-polymers00
Water48627
1
A: Synapse associated protein 97
C: 18-residue C-terminal peptide from glutamate receptor, ionotropic, AMPA1


Theoretical massNumber of molelcules
Total (without water)13,1162
Polymers13,1162
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-2 kcal/mol
Surface area5150 Å2
MethodPISA
2
B: Synapse associated protein 97


Theoretical massNumber of molelcules
Total (without water)11,3691
Polymers11,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.350, 54.310, 54.640
Angle α, β, γ (deg.)90.00, 84.03, 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: 11369.034 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 18-residue C-terminal peptide from glutamate receptor, ionotropic, AMPA1 / 18-residue C-terminal peptide from GluR-A


Mass: 1747.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic 18-residue peptide / References: GenBank: 29789269, UniProt: P19490*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 293 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 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2004
RadiationMonochromator: Diamond (111), germanium (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 48906 / Num. obs: 48906 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 2.2→2.33 Å / % possible obs: 91.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.78 / Num. measured obs: 7493 / Num. unique obs: 1485 / % possible all: 99.3

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Phasing

Phasing MRRfactor: 0.488 / Cor.coef. Fo:Fc: 0.478
Highest resolutionLowest resolution
Rotation3 Å34.16 Å
Translation3 Å34.16 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→34.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.055 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.326 509 5 %RANDOM
Rwork0.242 ---
all0.246 10167 --
obs0.246 10167 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: 48.035 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å2-5.11 Å2
2---0.75 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.21→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 0 27 1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221337
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.981805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6765183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5127.04544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93815225
X-RAY DIFFRACTIONr_chiral_restr0.1050.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02952
X-RAY DIFFRACTIONr_nbd_refined0.2370.2537
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.21
X-RAY DIFFRACTIONr_mcbond_it1.0171.5916
X-RAY DIFFRACTIONr_mcangle_it1.7621433
X-RAY DIFFRACTIONr_scbond_it2.2513449
X-RAY DIFFRACTIONr_scangle_it3.5344.5372
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 37 -
Rwork0.35 704 -
all-741 -
obs--100 %

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