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- EMDB-34674: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with g... -

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Basic information

Entry
Database: EMDB / ID: EMD-34674
TitleStructure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (minor class in symmetry)
Map data
Sample
  • Organelle or cellular component: Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2C
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNMDA receptor / GluN2C / MEMBRANE PROTEIN
Function / homology
Function and homology information


directional locomotion / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / 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 / positive regulation of Schwann cell migration / regulation of cell communication / 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 / transmitter-gated monoatomic ion channel activity / response to glycine / propylene metabolic process / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / glutamate binding / response to morphine / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / glycine binding / regulation of synapse assembly / response to amine / parallel fiber to Purkinje cell synapse / suckling behavior / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / positive regulation of calcium ion transport into cytosol / regulation of neuron apoptotic process / associative learning / cellular response to glycine / monoatomic cation transport / neuromuscular process controlling balance / excitatory synapse / social behavior / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / cellular response to manganese ion / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / synaptic cleft / prepulse inhibition / phosphatase binding / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / excitatory postsynaptic potential / regulation of membrane potential / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / synaptic membrane / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / negative regulation of protein catabolic process / cerebral cortex development / calcium ion transmembrane transport / visual learning / regulation of synaptic plasticity / calcium channel activity / response to wounding / long-term synaptic potentiation / memory / neuron cellular homeostasis / response to calcium ion / intracellular calcium ion homeostasis / terminal bouton / calcium ion transport / synaptic vesicle membrane / rhythmic process / synaptic vesicle / signaling receptor activity
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / Resolution: 4.3 Å
AuthorsZhang M / Zhang J / Guo F / Li Y / Zhu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
Citation
Journal: Nat Struct Mol Biol / Year: 2023
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: Journal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits
Authors: Zhang M / Zhu S
History
DepositionNov 4, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34674.png

Downloads & links

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Map

FileDownload / File: emd_34674.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 290 pix.
= 310.59 Å		1.07 Å/pix.
x 290 pix.
= 310.59 Å		1.07 Å/pix.
x 290 pix.
= 310.59 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.246
Minimum - Maximum-0.37193218 - 0.9909373
Average (Standard dev.)0.006784825 (±0.04938108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 310.59 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34674_half_map_1.map
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Half map: #1

Fileemd_34674_half_map_2.map
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Sample components

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Entire : Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate

EntireName: Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate
Components
  • Organelle or cellular component: Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2C
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate

SupramoleculeName: Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 89.724539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 WVRYQ

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2C

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2C / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 87.753758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Glutamate receptor ionotropic, NMDA 2C

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 8

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1
#0 - Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k)
#0 - Average electron dose: 60.0 e/Å2 / #1 - Image recording ID: 2
#1 - Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k)
#1 - Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing #1

Image processing ID1
Image recording ID1
Particle selectionNumber selected: 1188229
Startup model#0 - Type of model: OTHER / #1 - Type of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 15479
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 20 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Image recording ID2
Particle selectionNumber selected: 1188229
Startup model#0 - Type of model: OTHER / #1 - Type of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, RELION (ver. 3.1)) / Number images used: 15479
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.1)
Final 3D classificationNumber classes: 20 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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