+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7529 | ||||||||||||
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Title | GluN1-GluN2B NMDA receptors with exon 5 | ||||||||||||
Map data | GluN1-GluN2B NMDA receptor with exon 5 | ||||||||||||
Sample |
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Function / homology | Function and homology information pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / dendritic branch / conditioned taste aversion / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / dendritic branch / conditioned taste aversion / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / regulation of monoatomic cation transmembrane transport / voltage-gated monoatomic cation channel activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / NMDA glutamate receptor activity / parallel fiber to Purkinje cell synapse / NMDA selective glutamate receptor complex / response to morphine / calcium ion transmembrane import into cytosol / glutamate binding / neuromuscular process / protein heterotetramerization / positive regulation of calcium ion transport into cytosol / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / glycine binding / regulation of axonogenesis / regulation of dendrite morphogenesis / male mating behavior / suckling behavior / startle response / response to amine / regulation of neuronal synaptic plasticity / monoatomic cation transmembrane transport / associative learning / monoatomic cation transport / social behavior / excitatory synapse / ligand-gated monoatomic ion channel activity / positive regulation of excitatory postsynaptic potential / cellular response to glycine / positive regulation of dendritic spine maintenance / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to manganese ion / phosphatase binding / glutamate receptor binding / long-term memory / regulation of neuron apoptotic process / monoatomic cation channel activity / prepulse inhibition / calcium ion homeostasis / synaptic cleft / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sensory perception of pain / response to amphetamine / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / regulation of membrane potential / excitatory postsynaptic potential / learning / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / visual learning / calcium channel activity / response to organic cyclic compound / regulation of synaptic plasticity / terminal bouton / cerebral cortex development / memory / intracellular calcium ion homeostasis / synaptic vesicle membrane / response to calcium ion / neuron cellular homeostasis / calcium ion transport / rhythmic process / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / response to ethanol / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / dendritic spine / postsynaptic density / learning or memory Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||
Authors | Furukawa H / Grant T / Grigorieff N | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Neuron / Year: 2018 Title: Structural Mechanism of Functional Modulation by Gene Splicing in NMDA Receptors. Authors: Michael C Regan / Timothy Grant / Miranda J McDaniel / Erkan Karakas / Jing Zhang / Stephen F Traynelis / Nikolaus Grigorieff / Hiro Furukawa / Abstract: Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical ...Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical environment in the mammalian brain. Splice variants possessing the exon-5-encoded motif at the amino-terminal domain (ATD) of the GluN1 subunit are known to display robustly altered deactivation rates and pH sensitivity, but the underlying mechanism for this functional modification is largely unknown. Here, we show through cryoelectron microscopy (cryo-EM) that the presence of the exon 5 motif in GluN1 alters the local architecture of heterotetrameric GluN1-GluN2 NMDA receptors and creates contacts with the ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, which are absent in NMDA receptors lacking the exon 5 motif. The unique interactions established by the exon 5 motif are essential to the stability of the ATD/LBD and LBD/LBD interfaces that are critically involved in controlling proton sensitivity and deactivation. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7529.map.gz | 59.2 MB | EMDB map data format | |
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Header (meta data) | emd-7529-v30.xml emd-7529.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_7529.png | 23.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7529 | HTTPS FTP |
-Validation report
Summary document | emd_7529_validation.pdf.gz | 484.4 KB | Display | EMDB validaton report |
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Full document | emd_7529_full_validation.pdf.gz | 484 KB | Display | |
Data in XML | emd_7529_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_7529_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7529 | HTTPS FTP |
-Related structure data
Related structure data | 6cnaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7529.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GluN1-GluN2B NMDA receptor with exon 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GluN1-GluN2B NMDA receptor ion channel
Entire | Name: GluN1-GluN2B NMDA receptor ion channel |
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Components |
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-Supramolecule #1: GluN1-GluN2B NMDA receptor ion channel
Supramolecule | Name: GluN1-GluN2B NMDA receptor ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Glutamate receptor ionotropic, NMDA 1
Supramolecule | Name: Glutamate receptor ionotropic, NMDA 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Spodoptera frugiperda multiple nucleopolyhedrovirus |
-Supramolecule #3: Glutamate receptor ionotropic, NMDA 2B
Supramolecule | Name: Glutamate receptor ionotropic, NMDA 2B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Spodoptera frugiperda multiple nucleopolyhedrovirus |
-Macromolecule #1: Glutamate receptor ionotropic, NMDA 1
Macromolecule | Name: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 94.455906 KDa |
Recombinant expression | Organism: Spodoptera frugiperda multiple nucleopolyhedrovirus |
Sequence | String: KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLQATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKSK ...String: KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLQATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKSK KRNYENLDQL SYDNKRGPKA EKVLQFDPGT KNVTALLMEA RELEARVIIL SASEDDAATV YRAAAMLDMT GS GYVWLVG EREISGNALR YAPDGIIGLQ LINGKNESAH ISDAVGVVAQ AVHELLEKEN ITDPPRGCVG NTNIWKTGPL FKR VLMSSK YADGVTGRVE FNEDGDRKFA QYSIMNLQNR KLVQVGIYNG THVIPNDRKI IWPGGETEKP RGYQMSTRLK IVTI HQEPF VYVKPTMSDG TCKEEFTVNG DPVKKVICTG PNDTSPGSPR HTVPQCCYGF CIDLLIKLAR TMQFTYEVHL VADGK FGTQ ERVQNSNKKE WNGMMGELLS GQADMIVAPL TINNERAQYI EFSKPFKYQG LTILVKKEIP RSTLDSFMQP FQSTLW LLV GLSVHVVAVM LYLLDRFSPF GRFKVNSEEE EEDALTLSSA MWFSWGVLLN SGIGEGAPRS FSARILGMVW AGFAMII VA SYTANLAAFL VLDRPEERIT GINDPRLRNP SDKFIYATVK QSSVDIYFRR QVELSTMYRH MEKHNYESAA EAIQAVRD N KLHAFIWDSA VLEFEASQKC DLVTTGELFF RSGFGIGMRK DSPWKQQVSL SILKSHENGF MEDLDKTWVR YQECDSRSN APATLTCENM AGVFMIVAGG IVAGIFLIFI EIAYKSRA |
-Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B
Macromolecule | Name: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 91.160156 KDa |
Recombinant expression | Organism: Spodoptera frugiperda multiple nucleopolyhedrovirus |
Sequence | String: SIGIAVILVG TSDEVAIKDA HEKDDFHHLS VVPRVELVAM NETDPKSIIT RICDLMSDRK IQGVVFADDT DQEAIAQILD FISAQTLTP ILGIHGGSSM IMADKDESSM FFQFGPSIEQ QASVMLNIME EYDWYIFSIV TTYFPGYQDF VNKIRSTIEN S FVGWELEE ...String: SIGIAVILVG TSDEVAIKDA HEKDDFHHLS VVPRVELVAM NETDPKSIIT RICDLMSDRK IQGVVFADDT DQEAIAQILD FISAQTLTP ILGIHGGSSM IMADKDESSM FFQFGPSIEQ QASVMLNIME EYDWYIFSIV TTYFPGYQDF VNKIRSTIEN S FVGWELEE VLLLDMSLDD GDCKIQNQLK KLQSPIILLY CTKEEATYIF EVANSVGLTG YGYTWIVPSL VAGDTDTVPS EF PTGLISV SYDEWDYGLP ARVRDGIAII TTAASDMLSE HSFIPEPKSS CYNTHEKRIY QSNMLNRYLI NVTFEGRDLS FSE DGYQMH PKLVIILLNK ERKWERVGKW KDKSLQMKYY VWPRMCPETE EQEDDHLSIV TLEEAPFVIV ESVDPLSGTC MRNT VPCQK RIISENKTDE EPGYIKKCCK GFCIDILKKI SKSVKFTYDL YLVTNGKHGK KINGTWNGMI GEVVMKRAYM AVGSL TINE ERSEVVDFSV PFIETGISVM VSRSNGTVSP SAFLEPFSAC VWVMMFVMLL IVSAVAVFVF EYFSPVGYNR CLADGR EPG GPSFTIGKAI WLLWGLVFNN SVPVQNPKGT TSKIMVSVWA FFAVIFLASY TANLAAFMIQ EEYVDQVSGL SDKKFQR PN DFSPPFRFGT VPNGSTERNI RNNYAEMHAY MGKFNQRGVD DALLSLKTGK LDAFIYDAAV LNYMAGRDEG CKLVTIGS G KVFASTGYGI AIQKDSGWKR QVDLAILQLF GDGEMEELEA LWLTGICHNE KNEVMSSQLD IDNMAGVFYM LGAAMALSL ITFISEHLFY KS |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 10 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Concentration: 20.0 mM / Component - Name: HEPES |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 96.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73790 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |