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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
DescriptorIonotropic glutamate receptor subunit NR2B
chain F
(N-methyl-D-aspartate receptor subunit ...) x 2
KeywordsMEMBRANE PROTEIN / membrane protein
Specimen sourceXenopus laevis / amphibia / African clawed frog /
Mus musculus / mammal / ハツカネズミ, はつかねずみ /
MethodElectron microscopy (4.5 Å resolution / Particle / Single particle)
AuthorsLu, W. / Du, J. / Goehring, A. / Gouaux, E.
CitationScience, 2017, 355

Science, 2017, 355 StrPapers
Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation.
Wei Lü / Juan Du / April Goehring / Eric Gouaux

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 1, 2017 / Release: Mar 22, 2017

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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
MethodPISA

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Components

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

#1: Polypeptide(L)N-methyl-D-aspartate receptor subunit NR1-8a


Mass: 91639.867 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: C0KD18

Cellular component

Molecular function

  • extracellular-glutamate-gated ion channel activity (GO: 0005234)
  • ionotropic glutamate receptor activity (GO: 0004970)
#2: Polypeptide(L)N-methyl-D-aspartate receptor subunit NR2A


Mass: 93664.344 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis / References: UniProt: B7ZSK1

Cellular component

Molecular function

  • extracellular-glutamate-gated ion channel activity (GO: 0005234)
  • ionotropic glutamate receptor activity (GO: 0004970)

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Polypeptide(L) , 2 types, 3 molecules DFG

#3: Polypeptide(L)Ionotropic glutamate receptor subunit NR2B


Mass: 94552.234 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis / References: UniProt: A7XY94

Cellular component

Molecular function

  • extracellular-glutamate-gated ion channel activity (GO: 0005234)
  • ionotropic glutamate receptor activity (GO: 0004970)
#4: Polypeptide(L)GluN2B-specific Fab, termed 11D1


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

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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
#6: ChemicalChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 1 / Formula: C5H9NO4
#7: ChemicalChemComp-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

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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 FIELD
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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