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Yorodumi- PDB-5neb: Structure of GluK1 ligand-binding domain (S1S2) in complex with L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5neb | ||||||
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Title | Structure of GluK1 ligand-binding domain (S1S2) in complex with LM-12b at 2.05 A resolution | ||||||
Components | Glutamate receptor ionotropic, kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR / LIGAND-BINDING DOMAIN / GLUK1 / GLUR5 / AGONIST | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Moellerud, S. / Frydenvang, K. / Laulumaa, S. / Kastrup, J.S. | ||||||
Citation | Journal: ACS Chem Neurosci / Year: 2017 Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors. Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5neb.cif.gz | 221.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5neb.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 5neb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5neb_validation.pdf.gz | 480.2 KB | Display | wwPDB validaton report |
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Full document | 5neb_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 5neb_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 5neb_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5neb ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5neb | HTTPS FTP |
-Related structure data
Related structure data | 5nf5C 5nf6C 5ng9C 5nihC 5o4fC 4e0xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 29108.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER ...Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 (462) OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874). GLY1 IS A CLONING REMNANT. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami 2 / References: UniProt: P22756 |
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-Non-polymers , 6 types, 158 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate-citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9751 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9751 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→87.216 Å / Num. obs: 32564 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.68 Å2 / Rsym value: 0.067 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.487 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E0X Resolution: 2.05→50.65 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→50.65 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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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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