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- EMDB-33790: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with g... -

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Entry
Database: EMDB / ID: EMD-33790
TitleStructure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106
Map data
Sample
  • Organelle or cellular component: Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2C
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
  • Ligand: GLUTAMIC ACID
  • Ligand: 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
KeywordsNMDA receptor / GluN2C / MEMBRANE PROTEIN
Function / homology
Function and homology information


directional locomotion / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane / conditioned taste aversion / suckling behavior / olfactory learning ...directional locomotion / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane / conditioned taste aversion / suckling behavior / olfactory learning / neuromuscular process controlling balance / dendritic branch / response to glycoside / transmitter-gated monoatomic ion channel activity / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / RAF/MAP kinase cascade / neuromuscular process / neurotransmitter receptor complex / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA selective glutamate receptor complex / glutamate binding / regulation of axonogenesis / ligand-gated sodium channel activity / startle response / voltage-gated monoatomic cation channel activity / response to morphine / calcium ion transmembrane import into cytosol / regulation of synapse assembly / male mating behavior / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of dendrite morphogenesis / glycine binding / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / social behavior / regulation of neuronal synaptic plasticity / associative learning / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / cellular response to glycine / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / monoatomic cation transport / ligand-gated monoatomic ion channel activity / prepulse inhibition / phosphatase binding / long-term memory / adult locomotory behavior / calcium ion homeostasis / regulation of long-term neuronal synaptic plasticity / response to fungicide / monoatomic cation channel activity / sensory perception of pain / glutamate-gated receptor activity / cellular response to manganese ion / positive regulation of synaptic transmission, glutamatergic / response to amphetamine / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / visual learning / synaptic cleft / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / learning / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / synaptic membrane / sodium ion transmembrane transport / PDZ domain binding / synaptic transmission, glutamatergic / response to wounding / negative regulation of protein catabolic process / long-term synaptic potentiation / memory / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / response to calcium ion / regulation of synaptic plasticity / regulation of membrane potential / postsynaptic density membrane / intracellular calcium ion homeostasis / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / terminal bouton / synaptic vesicle membrane / rhythmic process / negative regulation of neuron apoptotic process / synaptic vesicle / amyloid-beta binding
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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 / cryo EM / Resolution: 3.0 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
DepositionJul 8, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33790.png

Downloads & links

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Map

FileDownload / File: emd_33790.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321.3 Å		1.07 Å/pix.
x 300 pix.
= 321.3 Å		1.07 Å/pix.
x 300 pix.
= 321.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.063066944 - 0.12811077
Average (Standard dev.)0.0002561402 (±0.0030136316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33790_half_map_1.map
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Half map: #1

Fileemd_33790_half_map_2.map
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Sample components

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

EntireName: Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106
Components
  • Organelle or cellular component: Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2C
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
  • Ligand: GLUTAMIC ACID
  • Ligand: 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

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

SupramoleculeName: 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
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: 97.574625 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 WVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQLEV LFQGPAAAHH HHHHHH

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: 13 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #7: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 7 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Macromolecule #8: methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethy...

MacromoleculeName: 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
Molecular weightTheoretical: 432.468 Da
Chemical component information

ChemComp-IWB:
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

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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

Concentration4.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 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

Particle selectionNumber selected: 2094482
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 601826
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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