+Open data
-Basic information
Entry | Database: PDB / ID: 5i56 | ||||||
---|---|---|---|---|---|---|---|
Title | Agonist-bound GluN1/GluN2A agonist binding domains with TCN201 | ||||||
Components | (Glutamate receptor ionotropic, NMDA ...) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist | ||||||
Function / homology | Function and homology information neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / serotonin metabolic process / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / sleep / voltage-gated monoatomic cation channel activity / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / locomotion / regulation of monoatomic cation transmembrane transport / response to morphine / cellular response to lipid / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / regulation of NMDA receptor activity / protein heterotetramerization / glutamate binding / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of axonogenesis / spinal cord development / dopamine metabolic process / suckling behavior / startle response / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / response to amine / modulation of excitatory postsynaptic potential / response to lithium ion / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / cellular response to glycine / positive regulation of dendritic spine maintenance / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of protein targeting to membrane / regulation of postsynaptic membrane potential / phosphatase binding / glutamate receptor binding / postsynaptic density, intracellular component / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / multicellular organismal response to stress / long-term memory / monoatomic cation channel activity / regulation of neuron apoptotic process / presynaptic active zone membrane / synaptic cleft / glutamate-gated receptor activity / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Mou, T.-C. / Sprang, S.R. / Hansen, K.B. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Neuron / Year: 2016 Title: Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors. Authors: Yi, F. / Mou, T.C. / Dorsett, K.N. / Volkmann, R.A. / Menniti, F.S. / Sprang, S.R. / Hansen, K.B. #1: Journal: To Be Published Title: Structural basis for negative allosteric modulation of GluN2A-containing NMDA receptors Authors: Yi, F. / Mou, T.-C. / Dorsett, K.N. / Sprang, S.R. / Hansen, K.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i56.cif.gz | 134 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i56.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 5i56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/5i56 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/5i56 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5i57C 5i58C 5i59C 5jtyC 4nf8S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33340.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439 |
---|---|
#2: Protein | Mass: 31533.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959 |
-Non-polymers , 4 types, 179 molecules
#3: Chemical | ChemComp-GLY / |
---|---|
#4: Chemical | ChemComp-GLU / |
#5: Chemical | ChemComp-67P / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | THE SEQUENCE CORRESPONDS TO THE NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A. RESIDUE THR242 IN ...THE SEQUENCE CORRESPOND |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.63 % / Description: rod |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate and 16-22% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.278→20.032 Å / Num. obs: 27522 / % possible obs: 96.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.61 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.49 / % possible all: 91.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NF8 Resolution: 2.28→20.03 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.16
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→20.03 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|