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- EMDB-27960: D-cycloserine and glutamate bound Human GluN1a-GluN2C NMDA recept... -

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Basic information

Entry
Database: EMDB / ID: EMD-27960
TitleD-cycloserine and glutamate bound Human GluN1a-GluN2C NMDA receptor in nanodisc - splayed conformation
Map dataB-factor sharpened map
Sample
  • Complex: Hetero-tetrameric GluN1a-GluN2C NMDA receptors
    • Protein or peptide: Ionotropic glutamate receptor, NMDA receptor GluN1a
    • Protein or peptide: Ionotropic glutamate receptor, NMDA receptor GluN2C
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsChou T-H / Furukawa H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural insights into assembly and function of GluN1-2C, GluN1-2A-2C, and GluN1-2D NMDARs.
Authors: Tsung-Han Chou / Hyunook Kang / Noriko Simorowski / Stephen F Traynelis / Hiro Furukawa /
Abstract: Neurotransmission mediated by diverse subtypes of N-methyl-D-aspartate receptors (NMDARs) is fundamental for basic brain functions and development as well as neuropsychiatric diseases and disorders. ...Neurotransmission mediated by diverse subtypes of N-methyl-D-aspartate receptors (NMDARs) is fundamental for basic brain functions and development as well as neuropsychiatric diseases and disorders. NMDARs are glycine- and glutamate-gated ion channels that exist as heterotetramers composed of obligatory GluN1 and GluN2(A-D) and/or GluN3(A-B). The GluN2C and GluN2D subunits form ion channels with distinct properties and spatio-temporal expression patterns. Here, we provide the structures of the agonist-bound human GluN1-2C NMDAR in the presence and absence of the GluN2C-selective positive allosteric potentiator (PAM), PYD-106, the agonist-bound GluN1-2A-2C tri-heteromeric NMDAR, and agonist-bound GluN1-2D NMDARs by single-particle electron cryomicroscopy. Our analysis shows unique inter-subunit and domain arrangements of the GluN2C NMDARs, which contribute to functional regulation and formation of the PAM binding pocket and is distinct from GluN2D NMDARs. Our findings here provide the fundamental blueprint to study GluN2C- and GluN2D-containing NMDARs, which are uniquely involved in neuropsychiatric disorders.
History
DepositionAug 26, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27960.png

Downloads & links

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Map

FileDownload / File: emd_27960.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Voxel sizeX=Y=Z: 0.856 Å
Density
Contour LevelBy AUTHOR: 0.349
Minimum - Maximum-0.971563 - 1.9961249
Average (Standard dev.)-0.0014981395 (±0.06860809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_27960_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_27960_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hetero-tetrameric GluN1a-GluN2C NMDA receptors

EntireName: Hetero-tetrameric GluN1a-GluN2C NMDA receptors
Components
  • Complex: Hetero-tetrameric GluN1a-GluN2C NMDA receptors
    • Protein or peptide: Ionotropic glutamate receptor, NMDA receptor GluN1a
    • Protein or peptide: Ionotropic glutamate receptor, NMDA receptor GluN2C

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Supramolecule #1: Hetero-tetrameric GluN1a-GluN2C NMDA receptors

SupramoleculeName: Hetero-tetrameric GluN1a-GluN2C NMDA receptors / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ionotropic glutamate receptor, NMDA receptor GluN1a

MacromoleculeName: Ionotropic glutamate receptor, NMDA receptor GluN1a / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTMHLLTFA LLFSCSFARA ASDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYAI LVSHPPTPND HFTPTPVSYT AGFYRIPVLG LTTRMSIYSD KSIHLSFLRT VPPYSHQSSV WFEMMRVYSW NHIILLVSDD ...String:
MSTMHLLTFA LLFSCSFARA ASDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYAI LVSHPPTPND HFTPTPVSYT AGFYRIPVLG LTTRMSIYSD KSIHLSFLRT VPPYSHQSSV WFEMMRVYSW NHIILLVSDD HEGRAAQKRL ETLLEERESK AEKVLQFDPG TKNVTALLME AKELEARVII LSASEDDAAT VYRAAAMLNM TGSGYVWLVG EREISGNALR YAPDGILGLQ LINGKNESAH ISDAVGVVAQ AVHELLEKEN ITDPPRGCVG NTNIWKTGPL FKRVLMSSKY ADGVTGRVEF NEDGDRKFAN YSIMNLQNRK LVQVGIYNGT HVIPNDRKII WPGGETEKPR GYQMSTRLKI VTIHQEPFVY VKPTLSDGTC KEEFTVNGDP VKKVICTGPN DTSPGSPRHT VPQCCYGFCI DLLIKLARTM NFTYEVHLVA DGKFGTQERV NNSNKKEWNG MMGELLSGQA DMIVAPLTIN NERAQYIEFS KPFKYQGLTI LVKKEIPRST LDSFMQPFQS TLWLLVGLSV HVVAVMLYLL DRFSPFGRFK VNSEEEEEDA LTLSSAMWFS WGVLLNSGIG EGAPRSFSAR ILGMVWAGFA MIIVASYTAN LAAFLVLDRP EERITGINDP RLRNPSDKFI YATVKQSSVD IYFRRQVELS TMYRHMEKHN YESAAEAIQA VRDNKLHAFI WDSAVLEFEA SQKCDLVTTG ELFFRSGFGI GMRKDSPWKQ NVSLSILKSH ENGFMEDLDK TWVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDANGAQ

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Macromolecule #2: Ionotropic glutamate receptor, NMDA receptor GluN2C

MacromoleculeName: Ionotropic glutamate receptor, NMDA receptor GluN2C / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGTMRLFLLA VLFLFSFARA TGWSHPQFEK GGGSGGGSGG SAWSHPQFEK GALVPRGEQG MTVAVVFSSS GPPQAQFRAR LTPQSFLDLP LEIQPLTVGV NTTNPSSLLT QICGLLGAAH VHGIVFEDNV DTEAVAQILD FISSQTHVPI LSISGGSAVV LTPKEPGSAF ...String:
MGTMRLFLLA VLFLFSFARA TGWSHPQFEK GGGSGGGSGG SAWSHPQFEK GALVPRGEQG MTVAVVFSSS GPPQAQFRAR LTPQSFLDLP LEIQPLTVGV NTTNPSSLLT QICGLLGAAH VHGIVFEDNV DTEAVAQILD FISSQTHVPI LSISGGSAVV LTPKEPGSAF LQLGVSLEQQ LQVLFKVLEE YDWSAFAVIT SLHPGHALFL EGVRAVADAS HVSWRLLDVV TLELGPGGPR ARTQRLLRQL DAPVFVAYCS REEAEVLFAE AAQAGLVGPG HVWLVPNLAL GSTDAPPATF PVGLISVVTE SWRLSLRQKV RDGVAILALG AHSYWRQHGT LPAPAGDCRV HPGPVSPARE AFYRHLLNVT WEGRDFSFSP GGYLVQPTMV VIALNRHRLW EMVGRWEHGV LYMKYPVWPR YSASLQPVVD SRHLTVATLE ERPFVIVESP DPGTGGCVPN TVPCRRQSNH TFSSGDVAPY TKLCCKGFCI DILKKLARVV KFSYDLYLVT NGKHGKRVRG VWNGMIGEVY YKRADMAIGS LTINEERSEI VDFSVPFVET GISVMVARSN GTVSPSAFLE PYSPAVWVMM FVMCLTVVAI TVFMFEYFSP VSYNQNLTRG KKSGGPAFTI GKSVWLLWAL VFNNSVPIEN PRGTTSKIMV LVWAFFAVIF LASYTANLAA FMIQEQYIDT VSGLSDKKFQ RPQDQYPPFR FGTVPNGSTE RNIRSNYRDM HTHMVKFNQR SVEDALTSLK MGKLDAFIYD AAVLNYMAGK DEGCKLVTIG SGKVFATTGY GIAMQKDSHW KRAIDLALLQ FLGDGETQKL ETVWLSGICQ NEKNEVMSSK LDIDNMAGVF YMLLVAMGLA LLVFAWEHLV YWKLRHSVPN

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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 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21674

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 111641
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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