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- EMDB-33790: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with g... -
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Open data
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Basic information
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Title | Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106 | |||||||||
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Function / homology | ![]() directional locomotion / 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 / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange ...directional locomotion / 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 / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / voltage-gated monoatomic cation channel activity / regulation of monoatomic cation transmembrane transport / response to morphine / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / 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 / monoatomic cation transport / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / ligand-gated monoatomic ion channel activity / neuromuscular process controlling balance / excitatory synapse / cellular response to glycine / positive regulation of dendritic spine maintenance / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / cellular response to manganese ion / glutamate receptor binding / long-term memory / prepulse inhibition / monoatomic cation channel activity / calcium ion homeostasis / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated calcium ion channel activity / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / excitatory postsynaptic potential / regulation of membrane potential / learning / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / long-term synaptic potentiation / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / visual learning / regulation of synaptic plasticity / calcium channel activity / negative regulation of protein catabolic process / terminal bouton / response to organic cyclic compound / memory / cerebral cortex development / synaptic vesicle membrane / response to wounding / intracellular calcium ion homeostasis / 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 Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Zhang M / Zhang J / Guo F / Li Y / Zhu S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits. Authors: Jilin Zhang / Ming Zhang / Qinrui Wang / Han Wen / Zheyi Liu / Fangjun Wang / Yuhang Wang / Fenyong Yao / Nan Song / Zengwei Kou / Yang Li / Fei Guo / Shujia Zhu / ![]() Abstract: N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di- ...N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di-heterotetramer (di-receptor), rat N1-N2C di-receptor and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a best resolution of 3.0 Å. The bilobate N-terminal domain (NTD) in N2D intrinsically adopts a closed conformation, leading to a compact NTD tetramer in the N1-N2D receptor. Additionally, crosslinking the ligand-binding domain (LBD) of two N1 protomers significantly elevated the channel open probability (Po) in N1-N2D di-receptors. Surprisingly, the N1-N2C di-receptor adopted both symmetric (minor) and asymmetric (major) conformations, the latter further locked by an allosteric potentiator, PYD-106, binding to a pocket between the NTD and LBD in only one N2C protomer. Finally, the N2A and N2C subunits in the N1-N2A-N2C tri-receptor display a conformation close to one protomer in the N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse function in major NMDA receptor subtypes. #1: ![]() Title: Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits Authors: Zhang M / Zhu S | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.4 KB 20.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 120.7 KB | ||
Others | ![]() ![]() | 80.7 MB 80.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yfhMC ![]() 7yffC ![]() 7yfgC ![]() 7yfiC ![]() 7yflC ![]() 7yfmC ![]() 7yfoC ![]() 7yfrC ![]() 8hdkC 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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Voxel size | X=Y=Z: 1.071 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33790_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33790_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate...
Entire | Name: Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106 |
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Components |
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-Supramolecule #1: Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate...
Supramolecule | Name: Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106 type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 97.574625 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS ...String: MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS DDHEGRAAQK RLETLLEERE SKAEKVLQFD PGTKNVTALL MEARELEARV IILSASEDDA ATVYRAAAML NM TGSGYVW LVGEREISGN ALRYAPDGII GLQLINGKNE SAHISDAVGV VAQAVHELLE KENITDPPRG CVGNTNIWKT GPL FKRVLM SSKYADGVTG RVEFNEDGDR KFANYSIMNL QNRKLVQVGI YNGTHVIPND RKIIWPGGET EKPRGYQMST RLKI VTIHQ EPFVYVKPTM SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCIDLLIK LARTMNFTYE VHLVA DGKF GTQERVNNSN KKEWNGMMGE LLSGQADMIV APLTINNERA QYIEFSKPFK YQGLTILVKK EIPRSTLDSF MQPFQS TLW LLVGLSVHVV AVMLYLLDRF SPFGRFKVNS EEEEEDALTL SSAMWFSWGV LLNSGIGEGA PRSFSARILG MVWAGFA MI IVASYTANLA AFLVLDRPEE RITGINDPRL RNPSDKFIYA TVKQSSVDIY FRRQVELSTM YRHMEKHNYE SAAEAIQA V RDNKLHAFIW DSAVLEFEAS QKCDLVTTGE LFFRSGFGIG MRKDSPWKQN VSLSILKSHE NGFMEDLDKT WVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQLEV LFQGPAAAHH HHHHHH |
-Macromolecule #2: Glutamate receptor ionotropic, NMDA 2C
Macromolecule | Name: Glutamate receptor ionotropic, NMDA 2C / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 87.753758 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGGALGPALL LTSLLGAWAR LGAGQGEQAV TVAVVFGSSG PLQTQARTRL TSQNFLDLPL EIQPLTVGVN NTNPSSILTQ ICGLLGAAR VHGIVFEDNV DTEAVAQLLD FVSSQTHVPI LSISGGSAVV LTPKEPGSAF LQLGVSLEQQ LQVLFKVLEE Y DWSAFAVI ...String: MGGALGPALL LTSLLGAWAR LGAGQGEQAV TVAVVFGSSG PLQTQARTRL TSQNFLDLPL EIQPLTVGVN NTNPSSILTQ ICGLLGAAR VHGIVFEDNV DTEAVAQLLD FVSSQTHVPI LSISGGSAVV LTPKEPGSAF LQLGVSLEQQ LQVLFKVLEE Y DWSAFAVI TSLHPGHALF LEGVRAVADA SYLSWRLLDV LTLELGPGGP RARTQRLLRQ VDAPVLVAYC SREEAEVLFA EA AQAGLVG PGHVWLVPNL ALGSTDAPPA AFPVGLISVV TESWRLSLRQ KVRDGVAILA LGAHSYRRQY GTLPAPAGDC RSH PGPVSP AREAFYRHLL NVTWEGRDFS FSPGGYLVRP TMVVIALNRH RLWEMVGRWD HGVLYMKYPV WPRYSTSLQP VVDS RHLTV ATLEERPFVI VESPDPGTGG CVPNTVPCRR QSNHTFSSGD LTPYTKLCCK GFCIDILKKL AKVVKFSYDL YLVTN GKHG KRVRGVWNGM IGEVYYKRAD MAIGSLTINE ERSEIIDFSV PFVETGISVM VSRSNGTVSP SAFLEPYSPA VWVMMF VMC LTVVAITVFM FEYFSPVSYN QNLTKGKKPG GPSFTIGKSV WLLWALVFNN SVPIENPRGT TSKIMVLVWA FFAVIFL AS YTANLAAFMI QEQYIDTVSG LSDKKFQRPQ DQYPPFRFGT VPNGSTERNI RSNYRDMHTH MVKFNQRSVE DALTSLKM G KLDAFIYDAA VLNYMAGKDE GCKLVTIGSG KVFATTGYGI AMQKDSHWKR AIDLALLQLL GDGETQKLET VWLSGICQN |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 13 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #6: GLYCINE
Macromolecule | Name: GLYCINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GLY |
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Molecular weight | Theoretical: 75.067 Da |
Chemical component information | ![]() ChemComp-GLY: |
-Macromolecule #7: GLUTAMIC ACID
Macromolecule | Name: GLUTAMIC ACID / type: ligand / ID: 7 / Number of copies: 2 / Formula: GLU |
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Molecular weight | Theoretical: 147.129 Da |
Chemical component information | ![]() ChemComp-GLU: |
-Macromolecule #8: methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethy...
Macromolecule | Name: methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethyl]-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-2-yl]benzoate type: ligand / ID: 8 / Number of copies: 1 / Formula: IWB |
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Molecular weight | Theoretical: 432.468 Da |
Chemical component information | ![]() ChemComp-IWB: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 9042 pixel / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |