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- EMDB-20964: Cryo-EM structure of Xenopus tropicalis pannexin 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-20964
TitleCryo-EM structure of Xenopus tropicalis pannexin 1
Map dataCryo-EM structure of Xenopus tropicalis pannexin 1
Sample
  • Complex: xenopus pannexin 1
    • Protein or peptide: Pannexin
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: HEXADECANE
Keywordsion channel / pannexin 1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of interleukin-1 production / gap junction / monoatomic cation transport / channel activity / monoatomic ion transmembrane transport / endoplasmic reticulum membrane / 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: 3.38 Å
AuthorsDeng Z / He Z
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structures of the ATP release channel pannexin 1.
Authors: Zengqin Deng / Zhihui He / Grigory Maksaev / Ryan M Bitter / Michael Rau / James A J Fitzpatrick / Peng Yuan /
Abstract: The plasma membrane adenosine triphosphate (ATP) release channel pannexin 1 (PANX1) has been implicated in many physiological and pathophysiological processes associated with purinergic signaling, ...The plasma membrane adenosine triphosphate (ATP) release channel pannexin 1 (PANX1) has been implicated in many physiological and pathophysiological processes associated with purinergic signaling, including cancer progression, apoptotic cell clearance, inflammation, blood pressure regulation, oocyte development, epilepsy and neuropathic pain. Here we present near-atomic-resolution structures of human and frog PANX1 determined by cryo-electron microscopy that revealed a heptameric channel architecture. Compatible with ATP permeation, the transmembrane pore and cytoplasmic vestibule were exceptionally wide. An extracellular tryptophan ring located at the outer pore created a constriction site, potentially functioning as a molecular sieve that restricts the size of permeable substrates. The amino and carboxyl termini, not resolved in the density map, appeared to be structurally dynamic and might contribute to narrowing of the pore during channel gating. In combination with functional characterization, this work elucidates the previously unknown architecture of pannexin channels and establishes a foundation for understanding their unique channel properties.
History
DepositionNov 15, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseApr 1, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uzy
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20964.png

Downloads & links

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Map

FileDownload / File: emd_20964.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Xenopus tropicalis pannexin 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.03
Minimum - Maximum-0.13275704 - 0.21938255
Average (Standard dev.)-0.000033253425 (±0.0068830918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1330.219-0.000

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Supplemental data

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Sample components

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Entire : xenopus pannexin 1

EntireName: xenopus pannexin 1
Components
  • Complex: xenopus pannexin 1
    • Protein or peptide: Pannexin
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: HEXADECANE

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Supramolecule #1: xenopus pannexin 1

SupramoleculeName: xenopus pannexin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)

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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: 49.735441 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
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 RDGLNSPVVS ENLQQSLWEI PLSHYKYPIV EQYLKTKNNS YGLIIKYLIC RVVTLIIVFT ACIYLGYYIS LF SLTDEFT CNIRTGILRN DTALPPLVQC KLIAVGVFRL LSYINLIIYV LIMPFIIYAM LVPFRKTANV LKVYEVLPTF SVQ QAPSKT YDDHSLFLLF LEENVSELKS YKFLKVLENI KNTGENFDTI QYLTSLGTVK TDTVDGKLAF KCTSEVPNNT EQNE VELTV QPSSDNAKTE EKKVRQRLLD SSCSNSLEVL FQ

UniProtKB: Pannexin

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Macromolecule #2: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 7 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #3: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 3 / Number of copies: 14 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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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

Concentration6 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176371
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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