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- EMDB-21150: Cryo-EM structure of Xenopus tropicalis pannexin 1 channel -

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Basic information

Entry
Database: EMDB / ID: EMD-21150
TitleCryo-EM structure of Xenopus tropicalis pannexin 1 channel
Map dataSharpened map of a pannexin1 channel
Sample
  • Complex: Heptameric pannexin1 complex assembly
    • Protein or peptide: Pannexin
Function / homology
Function and homology information


positive regulation of interleukin-1 production / gap junction / channel activity / monoatomic cation transport / identical protein binding / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
Biological speciesXenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsSyrjanen JL / Michalski M / Furukawa H / Kawate T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2020
Title: The Cryo-EM structure of pannexin 1 reveals unique motifs for ion selection and inhibition.
Authors: Kevin Michalski / Johanna L Syrjanen / Erik Henze / Julia Kumpf / Hiro Furukawa / Toshimitsu Kawate /
Abstract: Pannexins are large-pore forming channels responsible for ATP release under a variety of physiological and pathological conditions. Although predicted to share similar membrane topology with other ...Pannexins are large-pore forming channels responsible for ATP release under a variety of physiological and pathological conditions. Although predicted to share similar membrane topology with other large-pore forming proteins such as connexins, innexins, and LRRC8, pannexins have minimal sequence similarity to these protein families. Here, we present the cryo-EM structure of a frog pannexin 1 (Panx1) channel at 3.0 Å. We find that Panx1 protomers harbor four transmembrane helices similar in arrangement to other large-pore forming proteins but assemble as a heptameric channel with a unique constriction formed by Trp74 in the first extracellular loop. Mutating Trp74 or the nearby Arg75 disrupt ion selectivity, whereas altering residues in the hydrophobic groove formed by the two extracellular loops abrogates channel inhibition by carbenoxolone. Our structural and functional study establishes the extracellular loops as important structural motifs for ion selectivity and channel inhibition in Panx1.
History
DepositionDec 23, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseFeb 26, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.32
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vd7
  • Surface level: 3.32
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21150.png

Downloads & links

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Map

FileDownload / File: emd_21150.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of a pannexin1 channel
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 3.32 / Movie #1: 3.32
Minimum - Maximum-7.6881843 - 16.105282
Average (Standard dev.)0.007875091 (±0.69407773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-7.68816.1050.008

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Supplemental data

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Additional map: unsharpened map of a pannexin1 channel

Fileemd_21150_additional.map
Annotationunsharpened map of a pannexin1 channel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heptameric pannexin1 complex assembly

EntireName: Heptameric pannexin1 complex assembly
Components
  • Complex: Heptameric pannexin1 complex assembly
    • Protein or peptide: Pannexin

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Supramolecule #1: Heptameric pannexin1 complex assembly

SupramoleculeName: Heptameric pannexin1 complex assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Pannexin

MacromoleculeName: Pannexin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 39.424148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAIAHIATEY VFSDFLLKDP PESKYKGLRL ELAVDKLVSC IAVGLPLLLI SLAFAQEITL GSQISCFAPT SFSWRQAAYV DSFCWAAVQ QKHLSQSDSG NVPLWLHKFF PYILLLVAVL LYLPNLFWRF TAAPHLSSDL KFVMEELDKC YNRDIKDIKA A NNLNSSDK ...String:
MAIAHIATEY VFSDFLLKDP PESKYKGLRL ELAVDKLVSC IAVGLPLLLI SLAFAQEITL GSQISCFAPT SFSWRQAAYV DSFCWAAVQ QKHLSQSDSG NVPLWLHKFF PYILLLVAVL LYLPNLFWRF TAAPHLSSDL KFVMEELDKC YNRDIKDIKA A NNLNSSDK RDYPIVEQYL KTKNNSYGLI IKYLICRVVT LIIVFTACIY LGYYISLFSL TDEFTCNIRT GILRNDTALP PL VQCKLIA VGVFRLLSYI NLIIYVLIMP FIIYAMLVPF RKTANVLKVY EVLPTFSVQQ APSKTYDDHS LFLLFLEENV SEL KSYKFL KVLENIKASS WSHPQFEK

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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
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.3 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

CTF correctionSoftware - Name: Warp
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 90185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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