[English] 日本語
![](img/lk-miru.gif)
- PDB-1ddv: CRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ddv | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE HOMER EVH1 DOMAIN WITH BOUND MGLUR PEPTIDE | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / PROTEIN-LIGAND COMPLEX / POLYPROLINE RECOGNITION / BETA TURN | ||||||
Function / homology | ![]() : / : / PLC activating G protein-coupled glutamate receptor activity / : / regulation of translational elongation / negative regulation of locomotion / G protein-coupled glutamate receptor binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / structural constituent of postsynapse ...: / : / PLC activating G protein-coupled glutamate receptor activity / : / regulation of translational elongation / negative regulation of locomotion / G protein-coupled glutamate receptor binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / structural constituent of postsynapse / A2A adenosine receptor binding / regulation of dendritic spine maintenance / : / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / regulation of store-operated calcium entry / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / Neurexins and neuroligins / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / regulation of calcium ion import / protein localization to synapse / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / neuron spine / costamere / positive regulation of calcium ion transport / : / glutamate receptor activity / type 5 metabotropic glutamate receptor binding / G alpha (q) signalling events / postsynaptic cytosol / postsynaptic modulation of chemical synaptic transmission / plasma membrane => GO:0005886 / phosphatidylinositol-mediated signaling / behavioral response to cocaine / : / skeletal muscle contraction / positive regulation of protein tyrosine kinase activity / skeletal muscle fiber development / regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / response to cocaine / dendritic shaft / learning / locomotory behavior / PDZ domain binding / G protein-coupled receptor activity / protein tetramerization / postsynaptic density membrane / synapse organization / regulation of protein phosphorylation / regulation of long-term neuronal synaptic plasticity / response to nicotine / Schaffer collateral - CA1 synapse / cognition / Z disc / response to calcium ion / circadian rhythm / cellular response to amyloid-beta / apical part of cell / scaffold protein binding / postsynapse / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / dendritic spine / molecular adaptor activity / postsynaptic density / learning or memory / calmodulin binding / neuron projection / axon / protein phosphorylation / signaling receptor binding / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / regulation of DNA-templated transcription / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Beneken, J. / Tu, J.C. / Xiao, B. / Worley, P.F. / Leahy, D.J. | ||||||
![]() | ![]() Title: Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition. Authors: Beneken, J. / Tu, J.C. / Xiao, B. / Nuriya, M. / Yuan, J.P. / Worley, P.F. / Leahy, D.J. #1: ![]() Title: Homer binds a novel proline-rich motif and links group 1 metabotropic glutamate receptors with IP3 receptors Authors: Tu, J.C. / Xiao, B. / Yuan, J.P. / Lanahan, A.A. / Worley, P.F. / Leoffert, K. / Li, M. / Linden, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 35.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 24.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12688.221 Da / Num. of mol.: 1 / Fragment: HOMER EVH1 RESIDUES 1-111 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 644.715 Da / Num. of mol.: 1 / Fragment: MGLUR DERIVED PEPTIDE TPPSPF / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN NORWAY RAT (RATTUS NORVEGICUS) References: UniProt: P31424 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.46 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 7996 / Num. obs: 7996 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.377 / % possible all: 87 |
Reflection | *PLUS |
Reflection shell | *PLUS Mean I/σ(I) obs: 5.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.241 / Rfactor Rfree: 0.289 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|