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- PDB-5fxh: GluN1b-GluN2B NMDA receptor in non-active-1 conformation -

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Basic information

Entry
Database: PDB / ID: 5fxh
TitleGluN1b-GluN2B NMDA receptor in non-active-1 conformation
DescriptorN-METHYL-D-ASPARTATE RECEPTOR GLUN1
N-METHYL-D-ASPARTATE RECEPTOR GLUN2B
KeywordsTRANSPORT PROTEIN / SIGNALING PROTEIN / NMDA RECEPTOR / GLUTAMATE RECEPTOR / GLUN1 / GLUN2B / ION CHANNEL
Specimen sourceRattus norvegicus / mammal / NORWAY RAT / ドブネズミ, どぶねずみ /
MethodElectron microscopy (5 Å resolution / Particle / Single particle)
AuthorsTajima, N. / Karakas, E. / Grant, T. / Simorowski, N. / Diaz-Avalos, R. / Grigorieff, N. / Furukawa, H.
CitationNature, 2016, 534, 63-68

Nature, 2016, 534, 63-68 Yorodumi Papers
Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.
Nami Tajima / Erkan Karakas / Timothy Grant / Noriko Simorowski / Ruben Diaz-Avalos / Nikolaus Grigorieff / Hiro Furukawa

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2016 / Release: May 11, 2016
RevisionDateData content typeGroupProviderType
1.0May 11, 2016Structure modelrepositoryInitial release
1.1Jun 15, 2016Structure modelDatabase references
1.2Apr 19, 2017Structure modelOther

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Assembly

Deposited unit
A: N-METHYL-D-ASPARTATE RECEPTOR GLUN1
B: N-METHYL-D-ASPARTATE RECEPTOR GLUN2B
C: N-METHYL-D-ASPARTATE RECEPTOR GLUN1
D: N-METHYL-D-ASPARTATE RECEPTOR GLUN2B


Theoretical massNumber of molelcules
Total (without water)376,3044
Polyers376,3044
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)N-METHYL-D-ASPARTATE RECEPTOR GLUN1 / GLUN1 / GLUTAMATE NMDA RECEPTOR SUBUNIT ZETA-1 / N-METHYL-D-ASPARTATE RECEPTOR SUBUNIT NR1 / NMD-R1 / N-METHYL-D-ASPARTATE RECEPTOR GLUN1


Mass: 95220.727 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 23-868 / Mutation: YES
Source: (gene. exp.) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
References: UniProt: P35439

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)N-METHYL-D-ASPARTATE RECEPTOR GLUN2B / GLUN1 / GLUTAMATE NMDA RECEPTOR SUBUNIT ZETA-1 / N-METHYL-D-ASPARTATE RECEPTOR SUBUNIT NR1 / NMD-R1 / N-METHYL-D-ASPARTATE RECEPTOR GLUN1


Mass: 92931.078 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-852 / Mutation: YES
Source: (gene. exp.) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
References: UniProt: Q00960

Cellular component

Molecular function

Biological process

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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: NMDA RECEPTOR / Type: COMPLEX
Buffer solutionName: 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3
Details: 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3
pH: 7
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Aug 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated magnification: 38168 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SymmetryPoint symmetry: C2
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 15000 / Refinement type: HALF-MAPS REFINED AGAINST SAME DATA / Symmetry type: POINT
Least-squares processHighest resolution: 6.1 Å
Refine hist #LASTHighest resolution: 6.1 Å
Number of atoms included #LASTProtein: 15185 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 15185

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