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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1761 | |||||||||
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Title | Single particle analysis of PSD-95 in negative stain | |||||||||
![]() | 3d map of PSD-95 | |||||||||
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![]() | Scaffold protein / Membrane associated Guanylate Kinase / PDZ / SH3 | |||||||||
Function / homology | ![]() RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / cerebellar mossy fiber / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / frizzled binding / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / dendritic spine organization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / Synaptic adhesion-like molecules / positive regulation of dendrite morphogenesis / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / kinase binding / cell-cell adhesion / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / cell junction / cell-cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein phosphatase binding / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.9 Å | |||||||||
![]() | Fomina S / Howard TD / Sleator OK / Golovanova M / O'Ryan L / Leyland M / Grossmann JG / Collins RF / Prince SM | |||||||||
![]() | ![]() Title: Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95. Authors: Svetlana Fomina / Tina D Howard / Olivia K Sleator / Marina Golovanova / Liam O'Ryan / Mark L Leyland / J Günter Grossmann / Richard F Collins / Stephen M Prince / ![]() Abstract: The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using ...The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron micrographs corresponding to a 1:1 complex, a large self-enclosed tetrad complex and extended chains of linked channel domains. Using models derived from small angle X-ray scattering experiments in which high resolution structures from X-ray crystallographic and Nuclear Magnetic Resonance studies are positioned, the envelopes from single particle analysis can be resolved as a Kir2.1NC(4):PSD-95 complex and a tetrad of this unit (Kir2.1NC(4):PSD-95)(4). The tetrad complex shows the close association of the Kir2.1 cytoplasmic domains and the influence of PSD-95 mediated self-assembly on the clustering of these channels. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 216.6 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
Images | ![]() | 91 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xkxMC ![]() 1764C ![]() 1765C ![]() 1766C ![]() 2xkyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3d map of PSD-95 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.667 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Rat PSD-95
Entire | Name: Rat PSD-95 |
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Components |
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-Supramolecule #1000: Rat PSD-95
Supramolecule | Name: Rat PSD-95 / type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 1 |
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Molecular weight | Experimental: 95 KDa / Theoretical: 78 KDa / Method: SDS-PAGE |
-Macromolecule #1: PSD-95
Macromolecule | Name: PSD-95 / type: protein_or_peptide / ID: 1 / Name.synonym: PSD-95 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 95 KDa / Theoretical: 78 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | GO: neuronal ion channel clustering / InterPro: Disks large 1-like |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Details: 20mM Tris/HCl, 5mM DTT, 1mM EDTA, |
Staining | Type: NEGATIVE Details: Samples were adsorbed onto freshly glow discharged carbon film grids. Sample solution was pipetted into the grid followed by blotting, de-ionized water was then applied for 10s followed by ...Details: Samples were adsorbed onto freshly glow discharged carbon film grids. Sample solution was pipetted into the grid followed by blotting, de-ionized water was then applied for 10s followed by blotting, 2%w/v Uranyl Acetate solution was applied followed by a final blotting step. |
Grid | Details: 400 mesh Copper |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI 10 |
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Details | Low dose |
Image recording | Category: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 15 µm / Number real images: 2 / Details: none / Od range: 2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.6 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 43000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: PHILIPS ROTATION HOLDER |
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Image processing
Details | Particles selected using model based picking using an ab-initio model from Small angle X-ray scattering |
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CTF correction | Details: Paramters determined using Scattering curve |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 7854 |
Final two d classification | Number classes: 84 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | Model assembled using SAXS refinement and docked |
Refinement | Space: REAL |
Output model | ![]() PDB-2xkx: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | Model assembled using SAXS refinement and docked |
Refinement | Space: REAL |
Output model | ![]() PDB-2xkx: |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | Model assembled using SAXS refinement and docked |
Refinement | Space: REAL |
Output model | ![]() PDB-2xkx: |