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- EMDB-52105: CryoEM structure of dephosphorylated mouse Panx1 -

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Basic information

Entry
Database: EMDB / ID: EMD-52105
TitleCryoEM structure of dephosphorylated mouse Panx1
Map dataUnfiltered, unsharpened map from final refinement in cryoSPARC.
Sample
  • Complex: mouse Pannexin 1
    • Protein or peptide: Pannexin-1
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: 4.68 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_52105.png

Downloads & links

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Map

FileDownload / File: emd_52105.map.gz / Format: CCP4 / Size: 83.7 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.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.039832454 - 0.07616388
Average (Standard dev.)0.0011638495 (±0.0054727644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52105_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_52105_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map from post-processing in cryoSPARC.

Fileemd_52105_additional_1.map
AnnotationSharpened map from post-processing 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_52105_half_map_1.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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Half map: Half-map B from final refinement in cryoSPARC.

Fileemd_52105_half_map_2.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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Sample components

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Entire : mouse Pannexin 1

EntireName: mouse Pannexin 1
Components
  • Complex: mouse Pannexin 1
    • Protein or peptide: Pannexin-1

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Supramolecule #1: mouse Pannexin 1

SupramoleculeName: mouse Pannexin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The protein was dephosphorylated in vitro during purification.
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: 50.253176 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 YEILPTFDVL HFK SEGYND LSLYNLFLEE NISELKSYKC LKVLENIKSN GQGIDPMLLL TNLGMIKMDI IDGKIPTSLQ TKGEDQGSQR VEFK DLDLS SEAAANNGEK NSRQRLLNPS CGSAAAENLY FQGHHHHHH

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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
50.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
0.0002 m/vGDNglyco-diosgenin

Details: 150 mM NaCl, 50 mM HEPES at pH 8.0, 0.02% GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 20mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Detailspurified from Sf9

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 1590024
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: 4.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 94273
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-9hf2:
CryoEM structure of dephosphorylated mouse Panx1

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