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- PDB-5l1f: AMPA subtype ionotropic glutamate receptor GluA2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5l1f
TitleAMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor Perampanel
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN/INHIBITOR / Transporter / MEMBRANE PROTEIN / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / dendrite / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region ...Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6ZP / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsYelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Sobolevsky, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
CitationJournal: Neuron / Year: 2016
Title: Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs.
Authors: Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Narangoda, C. / Kurnikova, M. / Sobolevsky, A.I.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,50512
Polymers359,2234
Non-polymers2,2828
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27880 Å2
ΔGint-217 kcal/mol
Surface area135830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.740, 109.345, 594.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 89805.734 Da / Num. of mol.: 4
Fragment: UNP residues 25-847, with deletions of 397-398, 402-405, 566-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: BacMam / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P19491
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-6ZP / 2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile


Mass: 349.385 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H15N3O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11-14% (w/v) PEG 6,000, 0.1 M ammonium phosphate and 0.1 M TRIS (pH 7.9-8.0)
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4→49.57 Å / Num. obs: 51631 / % possible obs: 99.5 % / Observed criterion σ(I): 1.11 / Redundancy: 6.45 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.15
Reflection shellResolution: 4→4.14 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.9 / CC1/2: 0.49 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG2

3kg2


Resolution: 4→49.57 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 30.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 2581 5.01 %
Rwork0.2371 --
obs0.2388 51631 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23909 0 164 0 24073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224598
X-RAY DIFFRACTIONf_angle_d0.49733301
X-RAY DIFFRACTIONf_dihedral_angle_d9.17814476
X-RAY DIFFRACTIONf_chiral_restr0.0383741
X-RAY DIFFRACTIONf_plane_restr0.0034215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0005-4.04590.40781410.39682665X-RAY DIFFRACTION86
4.0459-4.09350.44731610.3993055X-RAY DIFFRACTION100
4.0935-4.14340.39161610.36493067X-RAY DIFFRACTION100
4.1434-4.19580.32231680.3453172X-RAY DIFFRACTION100
4.1958-4.2510.33841560.33572982X-RAY DIFFRACTION100
4.251-4.30920.33761640.33413130X-RAY DIFFRACTION100
4.3092-4.37070.34051640.29853140X-RAY DIFFRACTION99
4.3707-4.43590.34421590.29872969X-RAY DIFFRACTION100
4.4359-4.50520.26591660.28383096X-RAY DIFFRACTION100
4.5052-4.5790.30791640.26863158X-RAY DIFFRACTION100
4.579-4.65790.30011590.26863025X-RAY DIFFRACTION100
4.6579-4.74250.30891660.25443151X-RAY DIFFRACTION100
4.7425-4.83370.29871570.25753042X-RAY DIFFRACTION100
4.8337-4.93230.29641660.24523111X-RAY DIFFRACTION100
4.9323-5.03940.3131650.24233059X-RAY DIFFRACTION100
5.0394-5.15650.26861640.25013081X-RAY DIFFRACTION100
5.1565-5.28530.3131660.25563097X-RAY DIFFRACTION100
5.2853-5.42810.33661620.2443085X-RAY DIFFRACTION100
5.4281-5.58760.28181600.22623054X-RAY DIFFRACTION100
5.5876-5.76770.29741680.22793195X-RAY DIFFRACTION100
5.7677-5.97350.3091550.23553018X-RAY DIFFRACTION100
5.9735-6.21220.30251600.22343099X-RAY DIFFRACTION100
6.2122-6.49440.27421580.22293107X-RAY DIFFRACTION100
6.4944-6.83590.25121680.21273056X-RAY DIFFRACTION100
6.8359-7.2630.26121670.19593058X-RAY DIFFRACTION100
7.263-7.82180.25591650.19013106X-RAY DIFFRACTION100
7.8218-8.60520.21580.1753062X-RAY DIFFRACTION100
8.6052-9.8420.17271610.15843101X-RAY DIFFRACTION100
9.842-12.36790.16321640.17423066X-RAY DIFFRACTION100
12.3679-49.57340.35261650.30643084X-RAY DIFFRACTION99

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