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- EMDB-52106: CryoEM structure of mouse Panx1-Y308E -

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Basic information

Entry
Database: EMDB / ID: EMD-52106
TitleCryoEM structure of mouse Panx1-Y308E
Map dataUnfiltered, unsharpened map from final refinement in cryoSPARC.
Sample
  • Complex: mouse Pannexin 1 Y308E
    • Protein or peptide: Pannexin-1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water
KeywordsIon Channel / ATP release / MEMBRANE PROTEIN
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / The NLRP3 inflammasome / ATP transmembrane transporter activity / ATP transport / leak channel activity / positive regulation of interleukin-1 alpha production / bleb / monoatomic anion transmembrane transport / monoatomic anion channel activity / gap junction ...Electric Transmission Across Gap Junctions / The NLRP3 inflammasome / ATP transmembrane transporter activity / ATP transport / leak channel activity / positive regulation of interleukin-1 alpha production / bleb / monoatomic anion transmembrane transport / monoatomic anion channel activity / gap junction / gap junction channel activity / positive regulation of macrophage cytokine production / response to ATP / response to ischemia / positive regulation of interleukin-1 beta production / calcium channel activity / actin filament binding / calcium ion transport / cell-cell signaling / actin binding / protease binding / scaffold protein binding / transmembrane transporter binding / signaling receptor binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / protein-containing complex / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsZhang Q / Gaullier G / Mim C
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 21:1630 Sweden
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionNov 14, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52106.png

Downloads & links

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Map

FileDownload / File: emd_52106.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered, unsharpened map from final refinement in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 416 pix.
= 270.4 Å		0.65 Å/pix.
x 416 pix.
= 270.4 Å		0.65 Å/pix.
x 416 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.046289194 - 0.13089041
Average (Standard dev.)0.00061000604 (±0.0045794384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 270.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52106_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_52106_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map.

Fileemd_52106_additional_1.map
AnnotationSharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map obtained by postprocessing with deepEMhancer, using the...

Fileemd_52106_additional_2.map
AnnotationMap obtained by postprocessing with deepEMhancer, using the tightTarget weights.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B from final refinement in cryoSPARC.

Fileemd_52106_half_map_1.map
AnnotationHalf-map B from final refinement in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A from final refinement in cryoSPARC.

Fileemd_52106_half_map_2.map
AnnotationHalf-map A from final refinement in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse Pannexin 1 Y308E

EntireName: mouse Pannexin 1 Y308E
Components
  • Complex: mouse Pannexin 1 Y308E
    • Protein or peptide: Pannexin-1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water

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Supramolecule #1: mouse Pannexin 1 Y308E

SupramoleculeName: mouse Pannexin 1 Y308E / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 50.219117 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAIAHLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQ QKSSLQSESG NLPLWLHKFF PYILLLFAIL LYLPALFWRF SAAPHLCSDL KFIMEELDKV YNRAIKAAKS A RDLDLRDG ...String:
MAIAHLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQ QKSSLQSESG NLPLWLHKFF PYILLLFAIL LYLPALFWRF SAAPHLCSDL KFIMEELDKV YNRAIKAAKS A RDLDLRDG PGPPGVTENV GQSLWEISES HFKYPIVEQY LKTKKNSSHL IMKYISCRLV TFVVILLACI YLSYYFSLSS LS DEFLCSI KSGVLKNDST IPDRFQCKLI AVGIFQLLSL INLIVYALLI PVVVYTFFIP FRQKTDILKV EEILPTFDVL HFK SEGYND LSLYNLFLEE NISELKSYKC LKVLENIKSN GQGIDPMLLL TNLGMIKMDI IDGKIPTSLQ TKGEDQGSQR VEFK DLDLS SEAAANNGEK NSRQRLLNPS CGSAAAENLY FQGHHHHHH

UniProtKB: Pannexin-1

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 14 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 21 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
50.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
0.0002 m/vGDNglyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified from Sf9, 5mM FCC8 was added before freezing

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 957362
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model computed from the data by cryoSPARC
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 168845
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

jip4


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInteractive fitting in ChimeraX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9hf3:
CryoEM structure of mouse Panx1-Y308E

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