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- EMDB-8820: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2 -

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Basic information

Entry
Database: EMDB / ID: 8820
TitleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
SampleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
SourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Map dataGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Methodsingle particle reconstruction, at 4.4 Å resolution
AuthorsTwomey EC / Yelshanskaya MV
CitationNature, 2017

Nature, 2017 StrPapers
Channel opening and gating mechanism in AMPA-subtype glutamate receptors.
Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky

Validation ReportPDB-ID: 5wel

SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wel
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8820.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
0.98 Å/pix.
= 294. Å
300 pix
0.98 Å/pix.
= 294. Å
300 pix
0.98 Å/pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.98 Å
Density
Contour Level:0.026 (by author), 0.026 (movie #1):
Minimum - Maximum-0.06896673 - 0.13429308
Average (Standard dev.)0.000805433 (0.0049637896)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 294 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0690.1340.001

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Supplemental data

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Sample components

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Entire GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2

EntireName: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Number of components: 4

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Component #1: protein, GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2

ProteinName: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Recombinant expression: No
SourceSpecies: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Homo sapiens / human

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Component #2: protein, Chimera of Glutamate receptor 2, Germ cell-specific gene...

ProteinName: Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
Recombinant expression: No
MassTheoretical: 117.471211 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 #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, Digitonin

LigandName: Digitonin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.229312 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: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 67 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: 41926
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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