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- PDB-2g2l: Crystal Structure of the Second PDZ Domain of SAP97 in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 2g2l
TitleCrystal Structure of the Second PDZ Domain of SAP97 in Complex with a GluR-A C-terminal Peptide
Components
  • 18-mer peptide from glutamate receptor, ionotropic, AMPA1
  • Synapse-associated protein 97
KeywordsMEMBRANE PROTEIN / synaptic signaling / trafficking protein
Function / homology
Function and homology information


tissue morphogenesis / L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / hard palate development / structural constituent of postsynaptic density ...tissue morphogenesis / L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / hard palate development / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / astral microtubule organization / embryonic skeletal system morphogenesis / negative regulation of p38MAPK cascade / epithelial structure maintenance / reproductive structure development / immunological synapse formation / lateral loop / receptor localization to synapse / myelin sheath abaxonal region / peristalsis / smooth muscle tissue development / bicellular tight junction assembly / cortical microtubule organization / cell projection membrane / paranode region of axon / Trafficking of AMPA receptors / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / Activation of Ca-permeable Kainate Receptor / regulation of ventricular cardiac muscle cell action potential / positive regulation of potassium ion transport / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / cortical actin cytoskeleton organization / lens development in camera-type eye / regulation of myelination / ureteric bud development / neurotransmitter receptor localization to postsynaptic specialization membrane / ligand-gated monoatomic ion channel activity / branching involved in ureteric bud morphogenesis / positive regulation of actin filament polymerization / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / microvillus / kinesin binding / basement membrane / immunological synapse / Unblocking of NMDA receptors, glutamate binding and activation / bicellular tight junction / lateral plasma membrane / postsynaptic density, intracellular component / regulation of postsynaptic membrane neurotransmitter receptor levels / potassium channel regulator activity / phosphatase binding / T cell proliferation / ionotropic glutamate receptor binding / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of T cell proliferation / actin filament polymerization / T-tubule / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell activation / actin filament organization / basal plasma membrane / protein localization to plasma membrane / regulation of membrane potential / PDZ domain binding / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / neuromuscular junction / cerebral cortex development / cell-cell adhesion / cytoplasmic side of plasma membrane / kinase binding / synaptic vesicle membrane / negative regulation of epithelial cell proliferation / cell junction / intracellular protein localization / cell-cell junction / nervous system development / regulation of cell shape / signaling receptor activity / regulation of protein localization / presynaptic membrane / basolateral plasma membrane / chemical synaptic transmission / molecular adaptor activity / microtubule / transmembrane transporter binding / postsynaptic membrane / cell population proliferation / neuron projection
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 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / PDZ domain / Receptor, ligand binding region / Receptor family ligand binding region / 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 / Disks large homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
DepositionFeb 16, 2006Deposition 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 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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-mer peptide from glutamate receptor, ionotropic, AMPA1
D: 18-mer peptide from glutamate receptor, ionotropic, AMPA1


Theoretical massNumber of molelcules
Total (without water)26,4374
Polymers26,4374
Non-polymers00
Water79344
1
A: Synapse-associated protein 97
C: 18-mer peptide from glutamate receptor, ionotropic, AMPA1


Theoretical massNumber of molelcules
Total (without water)13,2182
Polymers13,2182
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-3 kcal/mol
Surface area5060 Å2
MethodPISA
2
B: Synapse-associated protein 97
D: 18-mer peptide from glutamate receptor, ionotropic, AMPA1


Theoretical massNumber of molelcules
Total (without water)13,2182
Polymers13,2182
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-2 kcal/mol
Surface area4940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.760, 54.440, 55.140
Angle α, β, γ (deg.)90.00, 93.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11471.255 Da / Num. of mol.: 2 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: DLG1_RAT / 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-mer peptide from glutamate receptor, ionotropic, AMPA1 / 18-mer peptide from GluRA18


Mass: 1747.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic 18-mer peptide / References: GenBank: 29789269, UniProt: M0R9A7*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, 30% PEG 4000 , 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) AND GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 8429 / Num. obs: 8429 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.35→2.45 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PDR

1pdr


Resolution: 2.35→38.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / SU B: 12.166 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29461 422 5 %RANDOM
Rwork0.21823 ---
all0.22196 ---
obs0.22196 8005 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: 45.075 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å25.83 Å2
2---1.86 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 0 44 1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221336
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.981805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.59526.66742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.415222
X-RAY DIFFRACTIONr_chiral_restr0.110.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02956
X-RAY DIFFRACTIONr_nbd_refined0.2570.2586
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0530.21
X-RAY DIFFRACTIONr_mcbond_it0.9551.5916
X-RAY DIFFRACTIONr_mcangle_it1.65121433
X-RAY DIFFRACTIONr_scbond_it2.1883453
X-RAY DIFFRACTIONr_scangle_it3.564.5372
LS refinement shellResolution: 2.353→2.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 31 -
Rwork0.319 580 -
obs--100 %

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