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- EMDB-31490: Human pannexin-1 showing a conformational change in the N-termina... -

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Basic information

Entry
Database: EMDB / ID: EMD-31490
TitleHuman pannexin-1 showing a conformational change in the N-terminal domain and blocked pore
Map data
Sample
  • Complex: human pannexin-1
    • Protein or peptide: Pannexin-1
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsATP release channel / vertebrate innexin homolog / TRANSPORT PROTEIN
Function / homology
Function and homology information


ATP transmembrane transporter activity / ATP transport / leak channel activity / Electric Transmission Across Gap Junctions / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / gap junction / monoatomic anion channel activity ...ATP transmembrane transporter activity / ATP transport / leak channel activity / Electric Transmission Across Gap Junctions / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / gap junction / monoatomic anion channel activity / gap junction channel activity / positive regulation of macrophage cytokine production / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / oogenesis / response to ATP / The NLRP3 inflammasome / monoatomic cation transport / positive regulation of interleukin-1 beta production / response to ischemia / calcium channel activity / calcium ion transport / actin filament binding / cell-cell signaling / protease binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / scaffold protein binding / transmembrane transporter binding / signaling receptor binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKuzuya M / Hirano H
CitationJournal: Sci Signal / Year: 2022
Title: Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.
Authors: Maki Kuzuya / Hidemi Hirano / Kenichi Hayashida / Masakatsu Watanabe / Kazumi Kobayashi / Tohru Terada / Md Iqbal Mahmood / Florence Tama / Kazutoshi Tani / Yoshinori Fujiyoshi / Atsunori Oshima /
Abstract: Pannexin (PANX) family proteins form large-pore channels that mediate purinergic signaling. We analyzed the cryo-EM structures of human PANX1 in lipid nanodiscs to elucidate the gating mechanism and ...Pannexin (PANX) family proteins form large-pore channels that mediate purinergic signaling. We analyzed the cryo-EM structures of human PANX1 in lipid nanodiscs to elucidate the gating mechanism and its regulation by the amino terminus in phospholipids. The wild-type channel has an amino-terminal funnel in the pore, but in the presence of the inhibitor probenecid, a cytoplasmically oriented amino terminus and phospholipids obstruct the pore. Functional analysis using whole-cell patch-clamp and oocyte voltage clamp showed that PANX1 lacking the amino terminus did not open and had a dominant negative effect on channel activity, thus confirming that the amino-terminal domain played an essential role in channel opening. These observations suggest that dynamic conformational changes in the amino terminus of human PANX1 are associated with lipid movement in and out of the pore. Moreover, the data provide insight into the gating mechanism of PANX1 and, more broadly, other large-pore channels.
History
DepositionJul 2, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-7f8n
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31490.png

Downloads & links

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Map

FileDownload / File: emd_31490.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 280 pix.
= 226.8 Å		0.81 Å/pix.
x 280 pix.
= 226.8 Å		0.81 Å/pix.
x 280 pix.
= 226.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.077172294 - 0.13060221
Average (Standard dev.)0.00005956101 (±0.0043093828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 226.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z226.800226.800226.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0770.1310.000

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Supplemental data

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Mask #1

Fileemd_31490_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_31490_half_map_1.map
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Half map: #1

Fileemd_31490_half_map_2.map
Projections & Slices
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Sample components

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Entire : human pannexin-1

EntireName: human pannexin-1
Components
  • Complex: human pannexin-1
    • Protein or peptide: Pannexin-1
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

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Supramolecule #1: human pannexin-1

SupramoleculeName: human pannexin-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pannexin-1

MacromoleculeName: Pannexin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.093863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQ QKNSLQSESG NLPLWLHKFF PYILLLFAIL LYLPPLFWRF AAAPHICSDL KFIMEELDKV YNRAIKAAKS A RDLDMRDG ...String:
MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQ QKNSLQSESG NLPLWLHKFF PYILLLFAIL LYLPPLFWRF AAAPHICSDL KFIMEELDKV YNRAIKAAKS A RDLDMRDG ACSVPGVTEN LGQSLWEVSE SHFKYPIVEQ YLKTKKNSNN LIIKYISCRL LTLIIILLAC IYLGYYFSLS SL SDEFVCS IKSGILRNDS TVPDQFQCKL IAVGIFQLLS VINLVVYVLL APVVVYTLFV PFRQKTDVLK VYEILPTFDV LHF KSEGYN DLSLYNLFLE ENISEVKSYK CLKVLENIKS SGQGIDPMLL LTNLGMIKMD VVDGKTPMSA EMREEQGNQT AELQ GMNID SETKANNGEK NARQRLLDSS C

UniProtKB: Pannexin-1

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Macromolecule #2: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 2 / Number of copies: 49 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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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

Concentration3.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMHEPES
300.0 mMNaClsodium chloride
GridModel: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA KF80

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 1083 / Average exposure time: 2.4 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 5.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 422244
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 19897
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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