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- PDB-4uqq: Electron density map of GluK2 desensitized state in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4uqq
TitleElectron density map of GluK2 desensitized state in complex with 2S,4R-4-methylglutamate
ComponentsGLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / ION CHANNEL
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / receptor clustering / modulation of excitatory postsynaptic potential / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / presynaptic modulation of chemical synaptic transmission / SNARE binding / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic synapse / 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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 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 1.4Oct 23, 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 / _pdbx_entry_details.has_protein_modification / _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
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  • Simplified surface model + fitted atomic model
  • EMDB-2685
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  • Superimposition on EM map
  • EMDB-2685
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2
B: GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2
C: GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2
D: GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,7868
Polymers398,1974
Non-polymers5894
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 IONOTROPIC, KAINATE 2 / GLUK2 / GLUTAMATE RECEPTOR 6 / GLUR-6 / GLUR6 / GLUK2


Mass: 99549.297 Da / Num. of mol.: 4 / Fragment: ATD LBD AND PARTIAL TMD, RESIDUES 32-908 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: I536V EXCHANGE DUE TO RNA EDITING / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P42260
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
Has protein modificationY
Sequence detailsLAST 5 RESIDUES ARE GENETICALLY ENGINEERED THROMBIN SITE

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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: GLUK2 / Type: COMPLEX
Buffer solutionName: 150 MM NACL, 20 MM TRIS, 1 MM 2S,4R-4- METHYLGLUTAMATE, 0.75 MM DDM
pH: 8
Details: 150 MM NACL, 20 MM TRIS, 1 MM 2S,4R-4- METHYLGLUTAMATE, 0.75 MM DDM
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 / Calibrated 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: EACH PARTICLE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 7.6 Å / Num. of particles: 21360
Details: COORDINATES FROM 3KG2 WERE FIT AS SEVEN INDEPENDENT RIGID BODIES CONSISTING OF TWO ATD DIMERS FROM PDB ID 3H6G FOUR LBD MONOMERS FROM PDB 3G3F AND A TMD TETRAMER FROM PDB 3KG2 GEOMETRY AND ...Details: COORDINATES FROM 3KG2 WERE FIT AS SEVEN INDEPENDENT RIGID BODIES CONSISTING OF TWO ATD DIMERS FROM PDB ID 3H6G FOUR LBD MONOMERS FROM PDB 3G3F AND A TMD TETRAMER FROM PDB 3KG2 GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE PRESENT IN PDB 3H6G 3G3F AND 3KG2 USED FOR RIGID BODY FITS SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2685. (DEPOSITION ID: 12610).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13H6G

3h6g

13H6G1PDBexperimental model
23G3F

3g3f

13G3F2PDBexperimental model
33KG2

3kg2

13KG23PDBexperimental model
RefinementHighest resolution: 7.6 Å
Refinement stepCycle: LAST / Highest resolution: 7.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22041 0 40 0 22081

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