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- EMDB-8579: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8579
TitleTriheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, MK-801 and a GluN2B-specific Fab, at pH 6.5
Map dataoriginal map
Sample
  • Complex: membrane protein
    • Protein or peptide: N-methyl-D-aspartate receptor subunit NR1-8aNMDA receptor
    • Protein or peptide: N-methyl-D-aspartate receptor subunit NR2ANMDA receptor
    • Protein or peptide: Ionotropic glutamate receptor subunit NR2B
    • Protein or peptide: GluN2B-specific Fab, termed 11D1
  • Ligand: GLUTAMIC ACID
  • Ligand: (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene
Function / homology
Function and homology information


glutamate-gated calcium ion channel activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / response to zinc ion / response to magnesium ion / late endosome / postsynaptic membrane / lysosome ...glutamate-gated calcium ion channel activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / response to zinc ion / response to magnesium ion / late endosome / postsynaptic membrane / lysosome / metal ion binding / plasma membrane
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 2B / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLu W / Du J / Goehring A / Gouaux E
CitationJournal: Science / Year: 2017
Title: Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation.
Authors: Wei Lü / Juan Du / April Goehring / Eric Gouaux /
Abstract: -methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B ...-methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B receptor in the absence or presence of the GluN2B-specific allosteric modulator Ro 25-6981 (Ro), determined by cryogenic electron microscopy (cryo-EM). In the absence of Ro, the GluN2A and GluN2B amino-terminal domains (ATDs) adopt "closed" and "open" clefts, respectively. Upon binding Ro, the GluN2B ATD clamshell transitions from an open to a closed conformation. Consistent with a predominance of the GluN2A subunit in ion channel gating, the GluN2A subunit interacts more extensively with GluN1 subunits throughout the receptor, in comparison with the GluN2B subunit. Differences in the conformation of the pseudo-2-fold-related GluN1 subunits further reflect receptor asymmetry. The triheteromeric NMDAR structures provide the first view of the most common NMDA receptor assembly and show how incorporation of two different GluN2 subunits modifies receptor symmetry and subunit interactions, allowing each subunit to uniquely influence receptor structure and function, thus increasing receptor complexity.
History
DepositionFeb 1, 2017-
Header (metadata) releaseFeb 22, 2017-
Map releaseMar 22, 2017-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5uow
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5uow
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8579.png

Downloads & links

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Map

FileDownload / File: emd_8579.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoriginal map
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.066 / Movie #1: 0.066
Minimum - Maximum-0.011001655 - 0.16992636
Average (Standard dev.)-0.00003394610 (±0.008436277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0110.170-0.000

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Supplemental data

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Additional map: sharpened map

Fileemd_8579_additional.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : membrane protein

EntireName: membrane protein
Components
  • Complex: membrane protein
    • Protein or peptide: N-methyl-D-aspartate receptor subunit NR1-8aNMDA receptor
    • Protein or peptide: N-methyl-D-aspartate receptor subunit NR2ANMDA receptor
    • Protein or peptide: Ionotropic glutamate receptor subunit NR2B
    • Protein or peptide: GluN2B-specific Fab, termed 11D1
  • Ligand: GLUTAMIC ACID
  • Ligand: (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene

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Supramolecule #1: membrane protein

SupramoleculeName: membrane protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: N-methyl-D-aspartate receptor subunit NR1-8a

MacromoleculeName: N-methyl-D-aspartate receptor subunit NR1-8a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 91.639867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DPKIVNIGAV LSTKKHEQIF REAVNQANKR HFTRKIQLNA TSVTHRPNAI QMALSVCEDL ISSQVYAILV SHPPAPTDHL TPTPISYTA GFYRIPVIGL TTRMSIYSDK SIHLSFLRTV PPYSHQALVW FEMMRLFNWN HVILIVSDDH EGRAAQKKLE T LLEEKESK ...String:
DPKIVNIGAV LSTKKHEQIF REAVNQANKR HFTRKIQLNA TSVTHRPNAI QMALSVCEDL ISSQVYAILV SHPPAPTDHL TPTPISYTA GFYRIPVIGL TTRMSIYSDK SIHLSFLRTV PPYSHQALVW FEMMRLFNWN HVILIVSDDH EGRAAQKKLE T LLEEKESK ADKVLQFEPG TKNLTALLLE AKELEARVII LSASEDDATA VYKSAAMLDM TGAGYVWLVG EREISGSALR YA PDGIIGL QLINGKNESA HISDAVAVVA QAIHELFEME QITDPPRGCV GNTNIWKTGP LFKRVLMSSK YPDGVTGRIE FNE DGDRKF AQYSIMNLQN RKLVQVGIFD GSYIIQNDRK IIWPGGETER PQGYQMSTRL KIVTIHQEPF VYVRPTTSDG TCRE EYTIN GDPIKKVICN GPDETIPGRP TVPQCCYGFC VDLLIKLARE MDFTYEVHLV ADGKFGTQER VNNSNAAAWN GMMGE LLSG QADMIVAPLT INNERAQYIE FSKPFKYQGL TILVKKEIPR STLDSFMQPF QSTLWLLVGL SVHVVAVMLY LLDRFS PFG RFKVNSAAAE EDALTLSSAM WFSWRVLLNS GLGEGAPRSF SARILGMVWA LFAMIIVASY TANLAAFLVL RRPEERI TG INDPRLRNPS DKFIYATVKQ SSVDIYFRRQ VELSTMYRHM EKHNYESAAE AIQAVRDNKL HAFIWDSAVL EFEASQDC D LVTTGELFFR SGFGIGMRKD SPWKQEVSLN ILKSHENGFM EELDKTWVRY QECDSRSNAP ATLTFENMAG VFYLVAGGI VAGIFLIFIE IAYK

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Macromolecule #2: N-methyl-D-aspartate receptor subunit NR2A

MacromoleculeName: N-methyl-D-aspartate receptor subunit NR2A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 93.664344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGMFVLLLYT FLYAGDLGHG AEKSFPVLNI AVILGRTRYI TERDIRSLWT RDMSLDFDVN VVTLLVQQTD PKSIITHVCD LMSGTKIHG VVFGDDTDQE AIAQILDFVS SQTFIPILGI HGGSSMIMAD KDEMSTFFQF GASIKQQATV MLNIMEEYDW H VFSVITSN ...String:
MGMFVLLLYT FLYAGDLGHG AEKSFPVLNI AVILGRTRYI TERDIRSLWT RDMSLDFDVN VVTLLVQQTD PKSIITHVCD LMSGTKIHG VVFGDDTDQE AIAQILDFVS SQTFIPILGI HGGSSMIMAD KDEMSTFFQF GASIKQQATV MLNIMEEYDW H VFSVITSN FPGYRDFISF IKTTVDNSFV GWEVQNYITL DTSYTDAQTL TQLKKIHSSV ILLYCSKDEA TYIFEEARSL GL MGYGFVW IVPSLVTGNT DIIPYEFPSG LVSVSYDDWD YGIEARVRDG LGIITTAASA MLEKHSVIPE AKTSCYGQNE RND PPLHTL HNFMINVTWD GKDLSFTEDG YQANPKLVVL LLNMEREWEK VGKWEAKSLN MKYPVWPRID SDHDDNHLSI VTLE EAPFV IVENIDYLTG TCVRNTVPCR KYFRLANSTT EGTSVKKCCK GFCIDILKKL SKTVKFTYDL YLVTNGKHGK KIKNV WNGM IGEVVYKRAV MAVGSLTINE ERSVAVDFSV PFVETGISVM VSRSAGTVSP SAFLEPFSAS VWVMMFVMLL LVSAMA VFI FEYFSPVGYN RNLAQGKDPH GPSFTIGKAV WLLWGLVFNN SLPVQNPKGT TSKIIVSIWA FFAVIFLASY TANLAAF MI QRRFVDQVTG LSDNKFQRPH DYSPPFRFGT VPQGSTERNI RNNYPDMHQY MVKFHQKGVQ DALVSLKTGK LDAFIYDA A VLNYMAGRDE GCKLVTIGSG YIFATTGYGI ALQKGSRWKR PIDLALLQFV GDGEMEELEK LWLTGICHTE KNEVMSSQL DIDNMAGVFY MLAAAMALSL ITFVWEHLFY KE

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Macromolecule #3: Ionotropic glutamate receptor subunit NR2B

MacromoleculeName: Ionotropic glutamate receptor subunit NR2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 94.552234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPTEACCYL KISLIILFYS RAYAQKHPNM DIAVILVGTT EEVAIKDVHE KDDFHHLPVT PRVELVTMQE SDPKSIITRI CDLMSDKKV QGVVFGDDTD QEAIAQILDF ISVQTLTPIL GIHGGSSMIM ADKEEASMFF QFGPSIEQQA SVMLNIMEEY D WYIFSIVT ...String:
MRPTEACCYL KISLIILFYS RAYAQKHPNM DIAVILVGTT EEVAIKDVHE KDDFHHLPVT PRVELVTMQE SDPKSIITRI CDLMSDKKV QGVVFGDDTD QEAIAQILDF ISVQTLTPIL GIHGGSSMIM ADKEEASMFF QFGPSIEQQA SVMLNIMEEY D WYIFSIVT TYFPGYQDFE NKVRSTIENS FVGWELEEVI HLDMSLDDID SKIQNQLKKL QSPVILLYCT KEEATYIFEV AH SVGLTGY GFTWIVPSLV AGDTDTVPDE FPTGLISVSY DEWDYDLPAR VRDGIAIITT AASTMLSEHN SIPQSKSSCN NIQ ESRVYE AHMLKRYLIN VTFEGRDLSF SEDGYQMHPK LVIILLNQER KWERVGKYKD RSLKMWPVFD LYPNSEEHKD EHLS IVTLE EAPFVIVEDV DPLSGTCMRN TVPCRKQIRP ENRTEEGGNY IKRCCKGFCI DILKKIAKTV KFTYDLYLVT NGKHG KKIN GVWNGMIGEV VTKRAYMAVG SLTINEERSE VVDFSVPFIE TGISVMVSRS NGTVSPSAFL EPFSADVWVM MFVMLL IVS AVAVFVFEYF SPVGYNRALA DGREPGGPSF TIGKAIWLLW GLVFNNSLPV QNPKGTTSKI MVSVWAFFAV IFLASYT AN LAAFMIQRRY VDQVSGLSDK KFQRPNDFSP AFRFGTVPNG STERNIRNNY LEMHSYMVKF NQRSVQDALL SLKSGKLD A FIYDAAVLNY MAGRDEGCKL VTIGSGKVFA TTGYGIAIQK DSGWKRQVDL AILQLFGDGE MEELEALWLT GICHNEKNE VMSSQLDIDN MAGVFYMLAA AMALSLITFI MEHLFYK

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Macromolecule #4: GluN2B-specific Fab, termed 11D1

MacromoleculeName: GluN2B-specific Fab, termed 11D1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.400619 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #6: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID / Glutamic acid

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Macromolecule #7: (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene

MacromoleculeName: (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene
type: ligand / ID: 7 / Number of copies: 1 / Formula: BMK
Molecular weightTheoretical: 221.297 Da
Chemical component information

ChemComp-BMK:
(5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene / neurotransmitter*YM / Dizocilpine

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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

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 0.84 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302052

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