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- PDB-5hfc: The third PDZ domain from the synaptic protein PSD-95 (H372A muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hfc | ||||||
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Title | The third PDZ domain from the synaptic protein PSD-95 (H372A mutant) in complex with a mutant C-terminal peptide derived from CRIPT (T-2F) | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / GLGF / DHR / adhesion / synapse / synaptic density / peptide-binding domain | ||||||
Function / homology | ![]() regulation of postsynaptic density protein 95 clustering / 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 / protein localization to microtubule / regulation of postsynaptic density assembly ...regulation of postsynaptic density protein 95 clustering / 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 / protein localization to microtubule / regulation of postsynaptic density assembly / 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 / postsynaptic density, intracellular component / positive regulation of synaptic transmission / glutamate receptor binding / cytoplasmic microtubule organization / ionotropic glutamate receptor binding / dendrite cytoplasm / RNA splicing / dendritic shaft / synaptic membrane / cell periphery / PDZ domain binding / postsynaptic density membrane / spliceosomal complex / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / kinase binding / cell-cell adhesion / mRNA processing / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / microtubule binding / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | White, K.I. / Raman, A.S. / Ranganathan, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Origins of Allostery and Evolvability in Proteins: A Case Study. Authors: Raman, A.S. / White, K.I. / Ranganathan, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5hebC ![]() 5hedC ![]() 5hetC ![]() 5heyC ![]() 5hf1C ![]() 5hfbC ![]() 5hffC ![]() 1be9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12670.998 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402) / Mutation: H372A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1116.266 Da / Num. of mol.: 1 / Fragment: PDZ3-binding domain (UNP residues 93-101) / Mutation: T99F / Source method: obtained synthetically Details: Synthesized using standard FMOC chemistry, HPCL purified, and lyophilized. Source: (synth.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.05 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of ...Details: Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.05 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (7 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.851→40.001 Å / Num. obs: 10760 / % possible obs: 98.22 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.543 |
Reflection shell | Resolution: 1.8514→1.9357 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BE9 Resolution: 1.851→40.001 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 20.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.851→40.001 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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