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- PDB-7qhh: Desensitized state of GluA1/2 AMPA receptor in complex with TARP-... -

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Basic information

Entry
Database: PDB / ID: 7qhh
TitleDesensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD)
Components
  • (Isoform Flip of Glutamate receptor ...) x 2
  • Voltage-dependent calcium channel gamma-8 subunit
KeywordsMEMBRANE PROTEIN / glutamate / AMPA receptor / TARPs
Function / homology
Function and homology information


Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / cellular response to ammonium ion / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / response to sucrose / regulation of monoatomic ion transmembrane transport ...Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / cellular response to ammonium ion / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / response to sucrose / regulation of monoatomic ion transmembrane transport / L-type voltage-gated calcium channel complex / cellular response to L-glutamate / myosin V binding / LGI-ADAM interactions / neuron spine / positive regulation of AMPA receptor activity / Trafficking of AMPA receptors / proximal dendrite / response to arsenic-containing substance / postsynaptic neurotransmitter receptor diffusion trapping / protein phosphatase 2B binding / cellular response to dsRNA / regulation of AMPA receptor activity / channel regulator activity / long-term synaptic depression / ligand-gated calcium channel activity / dendritic spine membrane / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / cellular response to peptide hormone stimulus / spinal cord development / regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / response to psychosocial stress / peptide hormone receptor binding / response to morphine / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / behavioral response to pain / perisynaptic space / neuronal cell body membrane / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / protein kinase A binding / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / regulation of receptor recycling / neuronal action potential / kainate selective glutamate receptor activity / response to electrical stimulus / adenylate cyclase binding / transmission of nerve impulse / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / cellular response to glycine / immunoglobulin binding / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / glutamate receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of synaptic transmission / conditioned place preference / long-term memory / regulation of synaptic transmission, glutamatergic / response to fungicide / postsynaptic density, intracellular component / voltage-gated calcium channel activity / extracellular ligand-gated monoatomic ion channel activity / cytoskeletal protein binding / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / synapse assembly / glutamate-gated calcium ion channel activity / somatodendritic compartment / presynaptic active zone membrane / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / excitatory synapse / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / cellular response to amino acid stimulus / positive regulation of excitatory postsynaptic potential / response to cocaine / calcium channel regulator activity / SNARE binding / dendritic shaft / synaptic membrane / establishment of protein localization / neuromuscular junction / synaptic transmission, glutamatergic / PDZ domain binding
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Voltage-dependent calcium channel, gamma-8 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Voltage-dependent calcium channel, gamma-8 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / GLUTAMIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITOLEIC ACID / Glutamate receptor 1 / Glutamate receptor 2 / Voltage-dependent calcium channel gamma-8 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHerguedas, B. / Kohegyi, B. / Dohrke, J.N. / Watson, J.F. / Zhang, D. / Ho, H. / Shaikh, S. / Lape, R. / Krieger, J.M. / Greger, I.H.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N002113/1 United Kingdom
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-106284GA-I00 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor.
Authors: Beatriz Herguedas / Bianka K Kohegyi / Jan-Niklas Dohrke / Jake F Watson / Danyang Zhang / Hinze Ho / Saher A Shaikh / Remigijus Lape / James M Krieger / Ingo H Greger /
Abstract: AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel ...AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop ('β1'), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance.
History
DepositionDec 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ncs_dom_lim
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

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  • Deposited structure unit
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  • EMDB-13972
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Isoform Flip of Glutamate receptor 1
B: Isoform Flip of Glutamate receptor 2
C: Isoform Flip of Glutamate receptor 1
D: Isoform Flip of Glutamate receptor 2
J: Voltage-dependent calcium channel gamma-8 subunit
I: Voltage-dependent calcium channel gamma-8 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,47324
Polymers484,9706
Non-polymers4,50318
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17J
27I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA - G390 - 901416
21THRTHRGLUGLUBB - K394 - 901415
12THRTHRGLUGLUAA - G390 - 901416
22THRTHRGLUGLUCC - N390 - 901416
13THRTHRGLUGLUAA - G390 - 901416
23THRTHRGLUGLUDD - R394 - 901415
14THRTHRGLUGLUBB - K394 - 901415
24THRTHRGLUGLUCC - N390 - 901416
15LYSLYSGLUGLUBB - K393 - 901414
25LYSLYSGLUGLUDD - R393 - 901414
16THRTHRGLUGLUCC - N390 - 901416
26THRTHRGLUGLUDD - R394 - 901415
17GLUGLUCYSCYSJE16 - 23516 - 235
27GLUGLUCYSCYSIF16 - 23516 - 235

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Isoform Flip of Glutamate receptor ... , 2 types, 4 molecules ACBD

#1: Protein Isoform Flip of Glutamate receptor 1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / ...GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1 / GluA1


Mass: 102661.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria1, Glur1 / Cell line (production host): HEK293 Expi / Production host: Homo sapiens (human) / References: UniProt: P19490
#2: Protein Isoform Flip of 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: 96247.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Cell line (production host): HEK293 Expi / Production host: Homo sapiens (human) / References: UniProt: P19491

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Protein , 1 types, 2 molecules JI

#3: Protein Voltage-dependent calcium channel gamma-8 subunit / Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein ...Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein gamma-8 / TARP gamma-8


Mass: 43576.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacng8 / Cell line (production host): HEK293 Expi / Production host: Homo sapiens (human) / References: UniProt: Q8VHW5

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Non-polymers , 4 types, 18 molecules

#4: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H30O2
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-79N / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36O4

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Details

Has ligand of interestY
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: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8
Type: COMPLEX
Details: GluA2 and TARP8 are expressed as a tandem construct
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.490 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 EXPI / Plasmid: PRK5
Buffer solutionpH: 8
Details: 25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was incubated with 87 uM CTZ for 30 minutes and 100 mM L-Glutamate was added before grid preparation
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3-4 second blots

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 340 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9664

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategoryDetails (eV)
2EPUimage acquisition
4GctfCTF correctionGctf was used to performed CTF correction
5RELION3.1CTF correctionCTF refinement was performed with relion
8Cootmodel fitting
9UCSF Chimeramodel fitting
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
15REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105918 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: First, rigid body fit was performed in Chimera using the coordinates of the TMD of 6QKC and the coordinates of the LBD in PDB code 3TKD. Manual model building was performed with Coot and ...Details: First, rigid body fit was performed in Chimera using the coordinates of the TMD of 6QKC and the coordinates of the LBD in PDB code 3TKD. Manual model building was performed with Coot and Refinement was performed with Refmac. The TMD and LBD maps obtained independently aided model building but were not used for refinement.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16QKC

6qkc

16QKC1PDBexperimental model
23TKD

3tkd

13TKD2PDBexperimental model
RefinementResolution: 3.6→339.2 Å / Cor.coef. Fo:Fc: 0.664 / SU B: 23.138 / SU ML: 0.306 / ESU R: 0.153
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.47551 --
obs0.47551 1752135 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 81.995 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.99 Å20 Å2
2---1.09 Å2-0 Å2
3---1.2 Å2
Refinement stepCycle: 1 / Total: 13622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01313902
ELECTRON MICROSCOPYr_bond_other_d00.01712100
ELECTRON MICROSCOPYr_angle_refined_deg1.2631.62818978
ELECTRON MICROSCOPYr_angle_other_deg1.3811.56427348
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.86351960
ELECTRON MICROSCOPYr_dihedral_angle_2_deg24.54120.433416
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.195151462
ELECTRON MICROSCOPYr_dihedral_angle_4_deg7.5841538
ELECTRON MICROSCOPYr_chiral_restr0.0550.21990
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0216362
ELECTRON MICROSCOPYr_gen_planes_other0.0020.023226
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.80211.4227906
ELECTRON MICROSCOPYr_mcbond_other2.80211.4217905
ELECTRON MICROSCOPYr_mcangle_it5.31217.1159844
ELECTRON MICROSCOPYr_mcangle_other5.31117.1179845
ELECTRON MICROSCOPYr_scbond_it1.3939.0075996
ELECTRON MICROSCOPYr_scbond_other1.3939.0065997
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.1314.1929135
ELECTRON MICROSCOPYr_long_range_B_refined16.28554678
ELECTRON MICROSCOPYr_long_range_B_other16.28554679
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A180720.16
12B180720.16
21A215660
22C215660
31A180740.16
32D180740.16
41B180720.16
42C180720.16
51B216520
52D216520
61C180740.16
62D180740.16
71J109440
72I109440
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.553 130198 -
obs--100 %

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