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- EMDB-7305: The Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic ... -

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Basic information

Entry
Database: EMDB / ID: 7305
TitleThe Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic Electron Microscopy
Map dataRaw unsharpened reconstruction of Kv Beta 2.1.
SampleOctamer of Kv Beta 2.1:
Kv Beta
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 4.9 Å resolution
AuthorsSpear JM / Mendez JH / Stagg SM
CitationJournal: To Be Published
Title: The Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic Electron Microscopy
Authors: Spear JM / Mendez JH / Danyuk Y / Stagg SM
DateDeposition: Dec 20, 2017 / Header (metadata) release: Jan 10, 2018 / Map release: Jan 30, 2019 / Last update: Jan 30, 2019

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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 radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7305.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
0.95 Å/pix.
= 228.72 Å
240 pix
0.95 Å/pix.
= 228.72 Å
240 pix
0.95 Å/pix.
= 228.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.953 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.009018989 - 0.03965336
Average (Standard dev.)0.00020069188 (0.004619418)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-119.0-119.0-119.0
Limit120.0120.0120.0
Spacing240240240
CellA=B=C: 228.72 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9530.9530.953
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z228.720228.720228.720
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-119-119-119
NC/NR/NS240240240
D min/max/mean-0.0090.0400.000

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Supplemental data

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Sample components

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Entire Octamer of Kv Beta 2.1

EntireName: Octamer of Kv Beta 2.1 / Number of components: 2

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Component #1: protein, Octamer of Kv Beta 2.1

ProteinName: Octamer of Kv Beta 2.1 / Recombinant expression: No
MassTheoretical: 360 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Kv Beta

ProteinName: Kv Beta / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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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: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D4 (2*4 fold dihedral) / Number of projections: 24809
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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