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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: EMD-7305
TitleThe Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic Electron Microscopy
Map dataRaw unsharpened reconstruction of Kv Beta 2.1.
Sample
  • Complex: Octamer of Kv Beta 2.1
    • Protein or peptide: Kv Beta
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon ...pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / regulation of potassium ion transmembrane transport / myoblast differentiation / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / neuron projection / axon / glutamatergic synapse / protein-containing complex binding / membrane / cytosol
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
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
History
DepositionDec 20, 2017-
Header (metadata) releaseJan 10, 2018-
Map releaseJan 30, 2019-
UpdateMay 15, 2019-
Current statusMay 15, 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 radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ci1
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7305.png

Downloads & links

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Map

FileDownload / File: emd_7305.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw unsharpened reconstruction of Kv Beta 2.1.
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.009018989 - 0.03965336
Average (Standard dev.)0.00020069188 (±0.004619418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-119-119-119
Dimensions240240240
Spacing240240240
CellA=B=C: 228.72 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ208208208
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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Additional map: None

Fileemd_7305_additional_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: None

Fileemd_7305_additional_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Independently masked half map

Fileemd_7305_half_map_1.map
AnnotationIndependently masked half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Independently masked half map

Fileemd_7305_half_map_2.map
AnnotationIndependently masked half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octamer of Kv Beta 2.1

EntireName: Octamer of Kv Beta 2.1
Components
  • Complex: Octamer of Kv Beta 2.1
    • Protein or peptide: Kv Beta

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Supramolecule #1: Octamer of Kv Beta 2.1

SupramoleculeName: Octamer of Kv Beta 2.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Kv Beta

MacromoleculeName: Kv Beta / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYPESTTGSP ARLSLRQTGS PGMIYSTRYG SPKRQLQFYR NLGKSGLRVS CLGLGTWVTF GGQITDEMAE HLMTLAYDN GINLFDTAEV YAAGKAEVVL GNIIKKKGWR RSSLVITTKI FWGGKAETER GLSRKHIIEG L KASLERLQ LEYVDVVFAN RPDPNTPMEE ...String:
MYPESTTGSP ARLSLRQTGS PGMIYSTRYG SPKRQLQFYR NLGKSGLRVS CLGLGTWVTF GGQITDEMAE HLMTLAYDN GINLFDTAEV YAAGKAEVVL GNIIKKKGWR RSSLVITTKI FWGGKAETER GLSRKHIIEG L KASLERLQ LEYVDVVFAN RPDPNTPMEE TVRAMTHVIN QGMAMYWGTS RWSSMEIMEA YSVARQFNLI PP ICEQAEY HMFQREKVEV QLPELFHKIG VGAMTWSPLA CGIVSGKYDS GIPPYSRASL KGYQWLKDKI LSE EGRRQQ AKLKELQAIA ERLGCTLPQL AIAWCLRNEG VSSVLLGASN AEQLMENIGA IQVLPKLSSS IVHE IDSIL GNKPYSKKDY RS

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Average electron dose: 60.0 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 reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24809
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6ci1:
The Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic Electron Microscopy

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