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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 / Cargo concentration in the ER / extrinsic component of synaptic membrane / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / cellular response to ammonium ion ...atrioventricular valve formation / neuronal signal transduction / Cargo concentration in the ER / extrinsic component of synaptic membrane / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / cellular response to ammonium ion / cardiac epithelial to mesenchymal transition / response to sucrose / proximal dendrite / myosin V binding / neuron spine / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / cellular response to L-glutamate / regulation of monoatomic ion transmembrane transport / conditioned place preference / response to arsenic-containing substance / cellular response to dsRNA / regulation of synapse structure or activity / dendritic spine membrane / Synaptic adhesion-like molecules / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / regulation of axon extension / extrinsic component of postsynaptic density membrane / response to morphine / neuronal cell body membrane / peptide hormone receptor binding / protein kinase A binding / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / response to psychosocial stress / spinal cord development / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / : / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / behavioral response to pain / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / adenylate cyclase binding / asymmetric synapse / regulation of receptor recycling / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / long-term memory / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / axonal growth cone / response to electrical stimulus / neuronal action potential / positive regulation of epithelial to mesenchymal transition / glutamate-gated receptor activity / response to fungicide / synapse assembly / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to amino acid stimulus / response to cocaine / synaptic membrane / response to nutrient levels / modulation of chemical synaptic transmission / postsynaptic density membrane / : / terminal bouton / neuromuscular junction / cellular response to growth factor stimulus / recycling endosome / cerebral cortex development / regulation of synaptic plasticity / small GTPase binding / receptor internalization / response to peptide hormone / long-term synaptic potentiation / response to toxic substance / synaptic vesicle membrane / recycling endosome membrane / synaptic vesicle / cell-cell junction / G-protein beta-subunit binding
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 Ca2+-permeable AMPA receptors
Authors: Fang C / Spangler CJ / Park J / Sheldon N / Trussell LO / Gouaux E
History
DepositionMar 14, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49723.png

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

Histogram

Histogram (log scale)
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49723_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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