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Open data
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Basic information
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Title | The structure of Noelin 1 with GluA1/A4-ATD | |||||||||
![]() | The structure of Noelin 1 with cerebellar GluA1/A4-ATD | |||||||||
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![]() | iGluR / CP-AMPA receptors / Noelin 1 / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / Cargo concentration in the ER / extrinsic component of synaptic membrane / axonal spine / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / COPII-mediated vesicle transport / cellular response to ammonium ion ...atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / Cargo concentration in the ER / extrinsic component of synaptic membrane / axonal spine / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / COPII-mediated vesicle transport / cellular response to ammonium ion / cardiac epithelial to mesenchymal transition / response to sucrose / neuron spine / myosin V binding / kainate selective glutamate receptor complex / Trafficking of AMPA receptors / proximal dendrite / regulation of monoatomic ion transmembrane transport / response to arsenic-containing substance / cellular response to dsRNA / cellular response to L-glutamate / regulation of synapse structure or activity / dendritic spine membrane / long-term synaptic depression / Synaptic adhesion-like molecules / beta-2 adrenergic receptor binding / regulation of axon extension / cellular response to peptide hormone stimulus / response to morphine / neuronal cell body membrane / protein kinase A binding / peptide hormone receptor binding / cellular response to amine stimulus / response to psychosocial stress / spinal cord development / Activation of AMPA receptors / perisynaptic space / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / behavioral response to pain / AMPA glutamate receptor complex / adenylate cyclase binding / ionotropic glutamate receptor complex / immunoglobulin binding / asymmetric synapse / conditioned place preference / excitatory synapse / response to electrical stimulus / regulation of receptor recycling / G-protein alpha-subunit binding / positive regulation of excitatory postsynaptic potential / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / positive regulation of synaptic transmission / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / positive regulation of epithelial to mesenchymal transition / axonal growth cone / neuronal action potential / response to fungicide / glutamate-gated receptor activity / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / synaptic membrane / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cocaine / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to amino acid stimulus / neuromuscular junction / response to nutrient levels / response to peptide hormone / postsynaptic density membrane / modulation of chemical synaptic transmission / recycling endosome / regulation of synaptic plasticity / cerebral cortex development / cellular response to growth factor stimulus / receptor internalization / small GTPase binding / response to toxic substance / long-term synaptic potentiation / terminal bouton / recycling endosome membrane / synaptic vesicle / synaptic vesicle membrane / cell-cell junction / G-protein beta-subunit binding / response to estradiol / presynapse Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | |||||||||
![]() | Fang CF / Gouaux E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Gating and noelin clustering of native Ca-permeable AMPA receptors. Authors: Chengli Fang / Cathy J Spangler / Jumi Park / Natalie Sheldon / Laurence O Trussell / Eric Gouaux / ![]() Abstract: AMPA-type ionotropic glutamate receptors (AMPARs) are integral to fast excitatory synaptic transmission and have vital roles in synaptic plasticity, motor coordination, learning and memory. Whereas ...AMPA-type ionotropic glutamate receptors (AMPARs) are integral to fast excitatory synaptic transmission and have vital roles in synaptic plasticity, motor coordination, learning and memory. Whereas extensive structural studies have been conducted on recombinant AMPARs and native calcium-impermeable (CI)-AMPARs alongside their auxiliary proteins, the molecular architecture of native calcium-permeable (CP)-AMPARs has remained undefined. Here, to determine the subunit composition, physiological architecture and gating mechanisms of CP-AMPARs, we visualize these receptors, immunoaffinity purified from rat cerebella, and resolve their structures using cryo-electron microscopy (cryo-EM). Our results indicate that the predominant assembly consists of GluA1 and GluA4 subunits, with the GluA4 subunit occupying the B and D positions, and auxiliary subunits, including transmembrane AMPAR regulatory proteins (TARPs) located at the B' and D' positions, and cornichon homologues (CNIHs) or TARPs located at the A' and C' positions. Furthermore, we resolved the structure of the noelin (NOE1)-GluA1-GluA4 complex, in which NOE1 specifically binds to the GluA4 subunit at the B and D positions. Notably, NOE1 stabilizes the amino-terminal domain layer without affecting gating properties of the receptor. NOE1 contributes to AMPAR function by forming dimeric AMPAR assemblies that are likely to engage in extracellular networks, clustering receptors in synaptic environments and modulating receptor responsiveness to synaptic inputs. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 324.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 77.5 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() ![]() | 171.1 MB 317.8 MB 317.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 981.9 KB | Display | ![]() |
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Full document | ![]() | 981.2 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9nr6MC ![]() 9nr7C ![]() 9nr8C ![]() 9nr9C ![]() 9nraC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | The structure of Noelin 1 with cerebellar GluA1/A4-ATD | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Additional Map
File | emd_49723_additional_1.map | ||||||||||||
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Annotation | Additional Map | ||||||||||||
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Density Histograms |
-Half map: Half Map B
File | emd_49723_half_map_1.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
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Density Histograms |
-Half map: Half Map A
File | emd_49723_half_map_2.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
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Density Histograms |
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Sample components
-Entire : CP-AMPA receptors
Entire | Name: CP-AMPA receptors |
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Components |
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-Supramolecule #1: CP-AMPA receptors
Supramolecule | Name: CP-AMPA receptors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Glutamate receptor 1
Macromolecule | Name: Glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 42.956734 KDa |
Sequence | String: ANFPNNIQIG GLFPNQQSQE HAAFRFALSQ LTEPPKLLPQ IDIVNISDSF EMTYRFCSQF SKGVYAIFGF YERRTVNMLT SFCGALHVC FITPSFPVDT SNQFVLQLRP ELQEALISII DHYKWQTFVY IYDADRGLSV LQRVLDTAAE KNWQVTAVNI L TTTEEGYR ...String: ANFPNNIQIG GLFPNQQSQE HAAFRFALSQ LTEPPKLLPQ IDIVNISDSF EMTYRFCSQF SKGVYAIFGF YERRTVNMLT SFCGALHVC FITPSFPVDT SNQFVLQLRP ELQEALISII DHYKWQTFVY IYDADRGLSV LQRVLDTAAE KNWQVTAVNI L TTTEEGYR MLFQDLEKKK ERLVVVDCES ERLNAILGQI VKLEKNGIGY HYILANLGFM DIDLNKFKES GANVTGFQLV NY TDTIPAR IMQQWRTSDS RDHTRVDWKR PKYTSALTYD GVKVMAEAFQ SLRRQRIDIS RRGNAGDCLA NPAVPWGQGI DIQ RALQQV RFEGLTGNVQ FNEKGRRTNY TLHVIEMKHD GIRKIGYWNE DDKFVPA UniProtKB: Glutamate receptor 1 |
-Macromolecule #2: Glutamate receptor 4
Macromolecule | Name: Glutamate receptor 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.087867 KDa |
Sequence | String: AFPSSVQIGG LFIRNTDQEY TAFRLAIFLH NTSPNASEAP FNLVPHVDNI ETANSFAVTN AFCSQYSRGV FAIFGLYDKR SVHTLTSFC SALHISLITP SFPTEGESQF VLQLRPSLRG ALLSLLDHYE WNCFVFLYDT DRGYSILQAI MEKAGQNGWH V SAICVENF ...String: AFPSSVQIGG LFIRNTDQEY TAFRLAIFLH NTSPNASEAP FNLVPHVDNI ETANSFAVTN AFCSQYSRGV FAIFGLYDKR SVHTLTSFC SALHISLITP SFPTEGESQF VLQLRPSLRG ALLSLLDHYE WNCFVFLYDT DRGYSILQAI MEKAGQNGWH V SAICVENF NDVSYRQLLE ELDRRQEKKF VIDCEIERLQ NILEQIVSVG KHVKGYHYII ANLGFKDISL ERFIHGGANV TG FQLVDFN TPMVTKLMDR WKKLDQREYP GSETPPKYTS ALTYDGVLVM AETFRSLRRQ KIDISRRGNA GDCLANPAAP WGQ GIDMER TLKQVRIQGL TGNVQFDHYG RRVNYTMDVF ELKSTGPRKV GYWNDMDKLV LI UniProtKB: Glutamate receptor 4 |
-Macromolecule #3: 11B8 scFv
Macromolecule | Name: 11B8 scFv / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 27.511527 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS SGGGGSGGGG SGGGGNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS ...String: EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS SGGGGSGGGG SGGGGNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS SFVHWYQQKP GQPPKLLIFL ASKLESGVPA RFSGSGSRTD FTLTIDPVEA DDAATYYCQQ TNEDPYTFGG GT KLEIKRA SNWSHPQFEK |
-Macromolecule #4: Noelin
Macromolecule | Name: Noelin / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.875629 KDa |
Sequence | String: YDELQSRVSN LEERLRACMQ KLACGKLTGI SDPVTVKTSG SRFGSWMTDP LAPEGDNRVW YMDGYHNNRF VREYKSMVDF MNTDNFTSH RLPHPWSGTG QVVYNGSIYF NKFQSHIIIR FDLKTETILK TRSLDYAGYN NMYHYAWGGH SDIDLMVDEN G LWAVYATN ...String: YDELQSRVSN LEERLRACMQ KLACGKLTGI SDPVTVKTSG SRFGSWMTDP LAPEGDNRVW YMDGYHNNRF VREYKSMVDF MNTDNFTSH RLPHPWSGTG QVVYNGSIYF NKFQSHIIIR FDLKTETILK TRSLDYAGYN NMYHYAWGGH SDIDLMVDEN G LWAVYATN QNAGNIVISK LDPVSLQILQ TWNTSYPKRS AGEAFIICGT LYVTNGYSGG TKVHYAYQTN ASTYEYIDIP FQ NKYSHIS MLDYNPKDRA LYAWNNGHQT LYNVTLFHVI UniProtKB: Noelin |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #8: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |