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- EMDB-0421: Structure of a Protein Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0421
TitleStructure of a Protein Complex
Map dataFully occupied GluA2 AMPA receptor - TARP complex bound with quisqualate and (R,R)-2b
Sample
  • Complex: Fully occupied GluA2 AMPA receptor - TARP complex bound with quisqualate and (R,R)-2b
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsZhao Y / Gouaux E
CitationJournal: To Be Published
Title: Structure of a Protein Complex
Authors: Zhao Y / Chen SS / Gouaux E
History
DepositionDec 10, 2018-
Header (metadata) releaseMar 27, 2019-
Map releaseDec 25, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0421.png

Downloads & links

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Map

FileDownload / File: emd_0421.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFully occupied GluA2 AMPA receptor - TARP complex bound with quisqualate and (R,R)-2b
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 320 pix.
= 550.4 Å		1.72 Å/pix.
x 320 pix.
= 550.4 Å		1.72 Å/pix.
x 320 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.019122977 - 0.0732789
Average (Standard dev.)0.00022590737 (±0.0022021586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z550.400550.400550.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0190.0730.000

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Supplemental data

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Sample components

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Entire : Fully occupied GluA2 AMPA receptor - TARP complex bound with quis...

EntireName: Fully occupied GluA2 AMPA receptor - TARP complex bound with quisqualate and (R,R)-2b
Components
  • Complex: Fully occupied GluA2 AMPA receptor - TARP complex bound with quisqualate and (R,R)-2b

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Supramolecule #1: Fully occupied GluA2 AMPA receptor - TARP complex bound with quis...

SupramoleculeName: Fully occupied GluA2 AMPA receptor - TARP complex bound with quisqualate and (R,R)-2b
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pCMVZeocin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris
0.1 % w/vdigitonindigitonin
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 130000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 10

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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