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- PDB-4uqj: Cryo-EM density map of GluA2em in complex with ZK200775 -

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Basic information

Entry
Database: PDB / ID: 4uqj
TitleCryo-EM density map of GluA2em in complex with ZK200775
ComponentsGLUTAMATE RECEPTOR 2
KeywordsTRANSPORT PROTEIN / GLUA2EM ANTAGONIST-BOUND CLOSED STATE
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / immunoglobulin binding / asymmetric synapse / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / somatodendritic compartment / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / PDZ domain binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / synaptic membrane / establishment of protein localization / postsynaptic density membrane / modulation of chemical synaptic transmission / cerebral cortex development / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / presynapse / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 I
Similarity search - Domain/homology
Chem-ZK1 / Glutamate receptor 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsMeyerson, J.R. / Kumar, J. / Chittori, S. / Rao, P. / Pierson, J. / Bartesaghi, A. / Mayer, M.L. / Subramaniam, S.
CitationJournal: Nature / Year: 2014
Title: Structural mechanism of glutamate receptor activation and desensitization.
Authors: Joel R Meyerson / Janesh Kumar / Sagar Chittori / Prashant Rao / Jason Pierson / Alberto Bartesaghi / Mark L Mayer / Sriram Subramaniam /
Abstract: Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the vertebrate brain. To gain a better understanding of how structural changes gate ion ...Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the vertebrate brain. To gain a better understanding of how structural changes gate ion flux across the membrane, we trapped rat AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) and kainate receptor subtypes in their major functional states and analysed the resulting structures using cryo-electron microscopy. We show that transition to the active state involves a 'corkscrew' motion of the receptor assembly, driven by closure of the ligand-binding domain. Desensitization is accompanied by disruption of the amino-terminal domain tetramer in AMPA, but not kainate, receptors with a two-fold to four-fold symmetry transition in the ligand-binding domains in both subtypes. The 7.6 Å structure of a desensitized kainate receptor shows how these changes accommodate channel closing. These findings integrate previous physiological, biochemical and structural analyses of glutamate receptors and provide a molecular explanation for key steps in receptor gating.
History
DepositionJun 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2680
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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)371,7318
Polymers370,0944
Non-polymers1,6374
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
GLUTAMATE RECEPTOR 2 / GLUR-2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K 2 / GLUTAMATE RECEPTOR IONOTROPIC / ...GLUR-2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K 2 / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 2 / GLUA2 / GLUA2


Mass: 92523.617 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-847 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P19491
#2: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: antagonist, medication*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GLUA2 / Type: COMPLEX
Buffer solutionName: 150 MM NACL, 20 MM TRIS, 0.75 MM DDM, 0.12 MM CHS, 0.3 MM ZK200775
pH: 8
Details: 150 MM NACL, 20 MM TRIS, 0.75 MM DDM, 0.12 MM CHS, 0.3 MM ZK200775
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2RELION3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 10.4 Å / Num. of particles: 26795
Details: COORDINATES FROM 3KG2 WERE FIT AS FIVE INDEPENDENT RIGID BODIES CONSISTING OF TWO ATD DIMERS AND TWO LBD DIMERS AND THE TMD. GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE PRESENT IN PDB ...Details: COORDINATES FROM 3KG2 WERE FIT AS FIVE INDEPENDENT RIGID BODIES CONSISTING OF TWO ATD DIMERS AND TWO LBD DIMERS AND THE TMD. GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE PRESENT IN PDB 3KG2 USED FOR RIGID BODY FITS SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2680. (DEPOSITION ID: 12574).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3KG2

3kg2


Accession code: 3KG2 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 10.4 Å
Refinement stepCycle: LAST / Highest resolution: 10.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21685 0 108 0 21793

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