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- EMDB-8581: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with ... -

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Basic information

Entry
Database: EMDB / ID: 8581
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
Samplemembrane protein
SourceXenopus laevis / amphibia / African clawed frog /
Map dataoriginal map
Methodsingle particle reconstruction, at 6 A resolution
AuthorsLu W / Du J / Goehring A
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

DateDeposition: Feb 1, 2017 / Header (metadata) release: Mar 22, 2017 / Map release: Mar 22, 2017 / Last update: Feb 1, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5up2
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8581.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.7 A/pix
= 435.2 A
256 pix
1.7 A/pix
= 435.2 A
256 pix
1.7 A/pix
= 435.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.7 A
Density
Contour Level:0.055 (by author), 0.055 (movie #1):
Minimum - Maximum-0.024976106 - 0.12082201
Average (Standard dev.)0.00058212783 (0.006057551)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 435.2 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0250.1210.001

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Supplemental data

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Sample components

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Entire membrane protein

EntireName: membrane protein / Number of components: 6

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Component #1: protein, membrane protein

ProteinName: membrane protein / Recombinant expression: No
SourceSpecies: Xenopus laevis / amphibia / African clawed frog /
Source (engineered)Expression System: Homo sapiens / human

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Component #2: protein, N-methyl-D-aspartate receptor subunit NR1-8a

ProteinName: N-methyl-D-aspartate receptor subunit NR1-8a / Recombinant expression: No
MassTheoretical: 94.056859 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #3: protein, N-methyl-D-aspartate receptor subunit NR2A

ProteinName: N-methyl-D-aspartate receptor subunit NR2A / Recombinant expression: No
MassTheoretical: 93.535227 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #4: protein, Ionotropic glutamate receptor subunit NR2B

ProteinName: Ionotropic glutamate receptor subunit NR2B / Recombinant expression: No
MassTheoretical: 94.552234 kDa
Source (engineered)Expression System: Xenopus laevis / amphibia / African clawed frog /

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Component #5: protein, GluN2B-specific Fab, termed 11D1

ProteinName: GluN2B-specific Fab, termed 11D1 / Recombinant expression: No
MassTheoretical: 18.400619 kDa
Source (engineered)Expression System: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Component #6: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.84 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 302052
3D reconstructionResolution: 6 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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