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- PDB-5uow: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5uow
TitleTriheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, MK-801 and a GluN2B-specific Fab, at pH 6.5
Components
  • (N-methyl-D-aspartate receptor subunit ...) x 2
  • GluN2B-specific Fab, termed 11D1
  • Ionotropic glutamate receptor subunit NR2B
KeywordsMEMBRANE PROTEIN / membrane protein
Function / homologyIonotropic glutamate receptor, metazoa / Receptor, ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal ...Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Ionotropic glutamate receptor / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to magnesium ion / extracellularly glutamate-gated ion channel activity / protein heterotetramerization / postsynaptic membrane / response to zinc ion / cell junction / intracellular / integral component of plasma membrane / metal ion binding / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 1
Function and homology information
Specimen sourceXenopus laevis / African clawed frog / amphibia / African clawed frog /
Mus musculus / House mouse / mammal /
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
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.
Copyright: 2017, American Association for the Advancement of Science.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 1, 2017 / Release: Mar 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Nov 8, 2017Structure modelAdvisory / Data collection / Derived calculationsem_image_scans / pdbx_struct_assembly / pdbx_unobs_or_zero_occ_atoms_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Assembly

Deposited unit
A: N-methyl-D-aspartate receptor subunit NR1-8a
B: N-methyl-D-aspartate receptor subunit NR2A
C: N-methyl-D-aspartate receptor subunit NR1-8a
D: Ionotropic glutamate receptor subunit NR2B
F: GluN2B-specific Fab, termed 11D1
G: GluN2B-specific Fab, termed 11D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,20524
Polyers408,2986
Non-polymers3,90818
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)25260
ΔGint (kcal/M)-203
Surface area (Å2)175740

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Components

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N-methyl-D-aspartate receptor subunit ... , 2 types, 3 molecules ACB

#1: Protein/peptide N-methyl-D-aspartate receptor subunit NR1-8a


Mass: 91639.867 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / Production host: Homo sapiens / References: UniProt:C0KD18, UniProt:A0A1L8F5J9*PLUS
#2: Protein/peptide N-methyl-D-aspartate receptor subunit NR2A


Mass: 93664.344 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis / Gene: LOC100127346 / Production host: Homo sapiens / References: UniProt:B7ZSK1

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Protein/peptide , 2 types, 3 molecules DFG

#3: Protein/peptide Ionotropic glutamate receptor subunit NR2B /


Mass: 94552.234 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis / Gene: NR2B / Production host: Homo sapiens / References: UniProt:A7XY94
#4: Protein/peptide GluN2B-specific Fab, termed 11D1


Mass: 18400.619 Da / Num. of mol.: 2 / Source: (gene. exp.) Mus musculus / Production host: Homo sapiens

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Non-polymers , 3 types, 18 molecules

#5: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 16 / Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 1 / Formula: C5H9NO4 / Glutamic acid
#7: Chemical ChemComp-BMK / (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene


Mass: 221.297 Da / Num. of mol.: 1 / Formula: C16H15N

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Details

Sequence detailsSample sequence for this chains is unknown

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: membrane protein / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: RECOMBINANT
Source (natural)Organism: Xenopus laevis
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 0.84 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 302052 / Symmetry type: POINT
Least-squares processHighest resolution: 4.5 Å

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