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- EMDB-8685: GluA2-0xGSG1L bound to ZK -

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Basic information

Entry
Database: EMDB / ID: 8685
TitleGluA2-0xGSG1L bound to ZK
SampleGluA2-0xGSG1L cryo-EM density
SourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Map dataGluA2-0xGSG1L bound to ZK
Methodsingle particle reconstruction, at 7.8 Å resolution
AuthorsTwomey EC / Yelshanskaya MV
CitationNeuron, 2017, 94, 569-580.e5

Neuron, 2017, 94, 569-580.e5 Yorodumi Papers
Structural Bases of Desensitization in AMPA Receptor-Auxiliary Subunit Complexes.
Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky

Validation ReportPDB-ID: 5vhw

SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.029
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.029
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5vhw
  • Surface level: 0.029
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8685.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.04 Å/pix.
= 374.4 Å
360 pix
1.04 Å/pix.
= 374.4 Å
360 pix
1.04 Å/pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.029 (by author), 0.029 (movie #1):
Minimum - Maximum-0.054082625 - 0.11139209
Average (Standard dev.)0.0003876232 (0.0033833603)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0540.1110.000

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Supplemental data

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Sample components

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Entire GluA2-0xGSG1L cryo-EM density

EntireName: GluA2-0xGSG1L cryo-EM density / Number of components: 4

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Component #1: protein, GluA2-0xGSG1L cryo-EM density

ProteinName: GluA2-0xGSG1L cryo-EM density / Recombinant expression: No
SourceSpecies: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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Component #2: protein, Glutamate receptor 2,Germ cell-specific gene 1-like protein

ProteinName: Glutamate receptor 2,Germ cell-specific gene 1-like protein
Recombinant expression: No
MassTheoretical: 117.471211 kDa
Source (engineered)Expression System: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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Component #3: ligand, {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihy...

LigandName: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.409254 kDa

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml / pH: 8
Support filmGold-gold grids, hydrogen and oxygen glow discharge (20s, 10 watts, 6.4 sccm H2, 27.5 sccm O2)
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 14372
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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