[English] 日本語
Yorodumi- PDB-6spz: Crystal structure of PDZ1-2 from PSD-95 with peptide ligand seque... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6spz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN / PSD-95 fragment / clustering / protein-complex / receptor-binding / membrane associated | ||||||
Function / homology | Function and homology information Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / LGI-ADAM interactions / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / P2Y1 nucleotide receptor binding ...Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / LGI-ADAM interactions / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / membrane repolarization during cardiac muscle cell action potential / regulation of resting membrane potential / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / AMPA glutamate receptor clustering / cellular response to potassium ion / regulation of membrane repolarization / cerebellar mossy fiber / Synaptic adhesion-like molecules / protein localization to synapse / vocalization behavior / intracellular potassium ion homeostasis / positive regulation of potassium ion transmembrane transport / neuron spine / membrane depolarization during cardiac muscle cell action potential / inward rectifier potassium channel activity / cardiac muscle cell action potential involved in contraction / juxtaparanode region of axon / neuron projection terminus / regulation of cardiac muscle cell contraction / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic ion transmembrane transport / acetylcholine receptor binding / Neurexins and neuroligins / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of Ca-permeable Kainate Receptor / relaxation of cardiac muscle / locomotory exploration behavior / cortical cytoskeleton / potassium ion import across plasma membrane / Signaling by ERBB4 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of heart rate by cardiac conduction / smooth endoplasmic reticulum / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / Long-term potentiation / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / intercalated disc / positive regulation of protein tyrosine kinase activity / rough endoplasmic reticulum / voltage-gated potassium channel complex / positive regulation of synaptic transmission / potassium ion transmembrane transport / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / learning / PDZ domain binding / postsynaptic density membrane / adherens junction / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / potassium ion transport / cell-cell adhesion / kinase binding / cellular response to mechanical stimulus / endocytic vesicle membrane / synaptic vesicle / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / RAF/MAP kinase cascade / scaffold protein binding / postsynaptic membrane / protein homotetramerization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Rodzli, N. / Levy, C.W. / Prince, S.M. | ||||||
Citation | Journal: Biophys.J. / Year: 2020 Title: The Dual PDZ Domain from Postsynaptic Density Protein 95 Forms a Scaffold with Peptide Ligand. Authors: Rodzli, N.A. / Lockhart-Cairns, M.P. / Levy, C.W. / Chipperfield, J. / Bird, L. / Baldock, C. / Prince, S.M. #1: Journal: Biorxiv / Year: 2019 Title: How the dual PDZ domain from Postsynaptic density protein 95 clusters ion channels and receptors. Authors: Rodzli, N. / Lockhart-Cairns, M.P. / Levy, C.W. / Chipperfield, J. / Bird, L. / Baldock, C. / Prince, S.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6spz.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6spz.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 6spz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/6spz ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6spz | HTTPS FTP |
---|
-Related structure data
Related structure data | 6spvC 3rl7S 3rl8S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains P Q) |
-Components
#1: Protein | Mass: 20868.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein/peptide | Mass: 790.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Syntheic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P63252*PLUS #3: Chemical | ChemComp-GSH / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % / Description: tetragonal bipyramid |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M NaCl, 0.1 M Na/K phosphate, 50% v/v PEG 200. Matrix microseeding with Apo crystal form (PDB ID: 6spv). |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→48.55 Å / Num. obs: 13236 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 980 / CC1/2: 0.762 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3rl7, 3rl8 Resolution: 2.08→48.549 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.386 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.225 / ESU R Free: 0.185 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.492 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→48.549 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
|