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- EMDB-30028: cryo-EM structure of human Pannexin 1 channel -

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Basic information

Entry
Database: EMDB / ID: EMD-30028
Titlecryo-EM structure of human Pannexin 1 channel
Map data
Sample
  • Complex: human pannexin protein 1
    • Protein or peptide: Pannexin-1
Keywordsion channel / molecular penetrate / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP transmembrane transporter activity / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / monoatomic anion channel activity / gap junction ...ATP transmembrane transporter activity / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / monoatomic anion channel activity / gap junction / 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 / response to ischemia / positive regulation of interleukin-1 beta production / calcium channel activity / actin filament binding / calcium ion transport / cell-cell signaling / protease binding / scaffold protein binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / 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: 3.2 Å
AuthorsRonggui Q / Lili D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2020
Title: Cryo-EM structure of human heptameric Pannexin 1 channel.
Authors: Ronggui Qu / Lili Dong / Jilin Zhang / Xuekui Yu / Lei Wang / Shujia Zhu /
History
DepositionFeb 19, 2020-
Header (metadata) releaseMar 25, 2020-
Map releaseMar 25, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m02
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30028.png

Downloads & links

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Map

FileDownload / File: emd_30028.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0285 / Movie #1: 0.0285
Minimum - Maximum-0.04409521 - 0.10844707
Average (Standard dev.)0.00043579953 (±0.0032170964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z334.400334.400334.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0440.1080.000

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Supplemental data

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Half map: #1

Fileemd_30028_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30028_half_map_2.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 : human pannexin protein 1

EntireName: human pannexin protein 1
Components
  • Complex: human pannexin protein 1
    • Protein or peptide: Pannexin-1

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Supramolecule #1: human pannexin protein 1

SupramoleculeName: human pannexin protein 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Eukaryota sp. (eukaryote)
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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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: GATAN K3 (6k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5740000000000003 µm / Calibrated defocus min: 0.503 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73421
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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