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- EMDB-49723: The structure of Noelin 1 with GluA1/A4-ATD -

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Basic information

Entry
Database: EMDB / ID: EMD-49723
TitleThe structure of Noelin 1 with GluA1/A4-ATD
Map dataThe structure of Noelin 1 with cerebellar GluA1/A4-ATD
Sample
  • Complex: CP-AMPA receptors
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Glutamate receptor 4
    • Protein or peptide: 11B8 scFv
    • Protein or peptide: Noelin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsiGluR / CP-AMPA receptors / Noelin 1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


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
Noelin domain / Neurogenesis glycoprotein / : / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Quinoprotein amine dehydrogenase, beta chain-like / Endoplasmic reticulum targeting sequence. / Ionotropic glutamate receptor, metazoa ...Noelin domain / Neurogenesis glycoprotein / : / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Quinoprotein amine dehydrogenase, beta chain-like / Endoplasmic reticulum targeting sequence. / 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
Glutamate receptor 1 / Glutamate receptor 4 / Noelin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFang CF / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
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
DepositionMar 14, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_49723.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of Noelin 1 with cerebellar GluA1/A4-ATD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 448 pix.
= 421.12 Å
0.94 Å/pix.
x 448 pix.
= 421.12 Å
0.94 Å/pix.
x 448 pix.
= 421.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.5791852 - 2.0388114
Average (Standard dev.)0.00034576008 (±0.03530475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 421.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_49723_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

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Half map: Half Map B

Fileemd_49723_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: Half Map A

Fileemd_49723_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : CP-AMPA receptors

EntireName: CP-AMPA receptors
Components
  • Complex: CP-AMPA receptors
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Glutamate receptor 4
    • Protein or peptide: 11B8 scFv
    • Protein or peptide: Noelin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: CP-AMPA receptors

SupramoleculeName: CP-AMPA receptors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor 1

MacromoleculeName: Glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 42.956734 KDa
SequenceString: 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

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Macromolecule #2: Glutamate receptor 4

MacromoleculeName: Glutamate receptor 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.087867 KDa
SequenceString: 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

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Macromolecule #3: 11B8 scFv

MacromoleculeName: 11B8 scFv / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.511527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #4: Noelin

MacromoleculeName: Noelin / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 31.875629 KDa
SequenceString: 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

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143111
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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