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- PDB-5up2: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5up2
TitleTriheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, Ro 25-6981, MK-801 and a GluN2B-specific Fab, at pH 6.5
DescriptorIonotropic glutamate receptor subunit NR2B
chainF
(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 (6 Å resolution / Particle / Single particle)
AuthorsLu, W. / Du, J. / Goehring, A. / Gouaux, E.
CitationScience, 2017, 355

Science, 2017, 355 Yorodumi Papers
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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Mar 29, 2017Structure modelNon-polymer description
1.2Apr 5, 2017Structure modelDatabase references
1.3Apr 26, 2017Structure modelOther
1.4Nov 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)414,99315
Polyers413,0026
Non-polymers1,9919
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)21030
ΔGint (kcal/M)-182
Surface area (Å2)179480

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Components

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


Mass: 94056.859 Da / Num. of mol.: 2
Source: (gene. exp.) Xenopus laevis / amphibia / African clawed frog /
References: UniProt: C0KD18

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)N-methyl-D-aspartate receptor subunit NR2A


Mass: 93535.227 Da / Num. of mol.: 1
Source: (gene. exp.) Xenopus laevis / amphibia / African clawed frog /
References: UniProt: B7ZSK1

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)GluN2B-specific Fab, termed 11D1


Mass: 18400.619 Da / Num. of mol.: 2
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#5: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 9 / Formula: C8H15NO6
Sequence detailsChain F and G is a GluN2B-specific Fab, termed 11D1. Sequence 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: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 302052 / Symmetry type: POINT

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