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- EMDB-62478: Cryo-EM structure of human pannexin-3 protomer -

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Basic information

Entry
Database: EMDB / ID: EMD-62478
TitleCryo-EM structure of human pannexin-3 protomer
Map data
Sample
  • Complex: Pannexin-3 protomer
    • Protein or peptide: Pannexin-3
KeywordsPannexin / Innexin / TRANSPORT PROTEIN
Function / homology
Function and homology information


gap junction hemi-channel activity / wide pore channel activity / positive regulation of interleukin-1 production / gap junction / monoatomic cation transport / calcium channel activity / osteoblast differentiation / cell-cell signaling / endoplasmic reticulum membrane / structural molecule activity / 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
AuthorsTsuyama T / Yokoyama K
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Japan Society for the Promotion of Science (JSPS)20J01396 Japan
Japan Society for the Promotion of Science (JSPS)20K06514 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Biochem Biophys Res Commun / Year: 2025
Title: Cryo-EM structure of the human Pannexin-3 channel.
Authors: Taiichi Tsuyama / Ryuga Teramura / Kaoru Mitsuoka / Jun-Ichi Kishikawa / Ken Yokoyama /
Abstract: Pannexin-3 (PANX3) is a member of the pannexin family of large-pore, ATP-permeable channels conserved across vertebrates. PANX3 contributes to various developmental and pathophysiological processes ...Pannexin-3 (PANX3) is a member of the pannexin family of large-pore, ATP-permeable channels conserved across vertebrates. PANX3 contributes to various developmental and pathophysiological processes by permeating ATP and Ca ions; however, the structural basis of PANX3 channel function remains unclear. Here, we present the cryo-EM structure of human PANX3 at 2.9-3.2 Å. The PANX3 channel is heptameric and forms a transmembrane pore along the central symmetric axis. The narrowest constriction of the pore is composed of an isoleucine ring located in the extracellular region, and its size is comparable to that of other pannexins. A structural variability analysis revealed prominent structural dynamics in intracellular regions. Our structural studies provide a foundation for understanding the detailed properties of pannexin channels.
History
DepositionNov 20, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62478.png

Downloads & links

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Map

FileDownload / File: emd_62478.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.472464 - 2.2602575
Average (Standard dev.)0.0013941915 (±0.05165743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62478_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_62478_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62478_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pannexin-3 protomer

EntireName: Pannexin-3 protomer
Components
  • Complex: Pannexin-3 protomer
    • Protein or peptide: Pannexin-3

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Supramolecule #1: Pannexin-3 protomer

SupramoleculeName: Pannexin-3 protomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pannexin-3

MacromoleculeName: Pannexin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.965449 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLAHTAAEY MLSDALLPDR RGPRLKGLRL ELPLDRIVKF VAVGSPLLLM SLAFAQEFSS GSPISCFSPS NFSIRQAAYV DSSCWDSLL HHKQDGPGQD KMKSLWPHKA LPYSLLALAL LMYLPVLLWQ YAAVPALSSD LLFIISELDK SYNRSIRLVQ H MLKIRQKS ...String:
MSLAHTAAEY MLSDALLPDR RGPRLKGLRL ELPLDRIVKF VAVGSPLLLM SLAFAQEFSS GSPISCFSPS NFSIRQAAYV DSSCWDSLL HHKQDGPGQD KMKSLWPHKA LPYSLLALAL LMYLPVLLWQ YAAVPALSSD LLFIISELDK SYNRSIRLVQ H MLKIRQKS SDPYVFWNEL EKARKERYFE FPLLERYLAC KQRSHSLVAT YLLRNSLLLI FTSATYLYLG HFHLDVFFQE EF SCSIKTG LLSDETHVPN LITCRLTSLS IFQIVSLSSV AIYTILVPVI IYNLTRLCRW DKRLLSVYEM LPAFDLLSRK MLG CPINDL NVILLFLRAN ISELISFSWL SVLCVLKDTT TQKHNIDTVV DFMTLLAGLE PSKPKHLTNS ACDEHPGSGG SGHH HHHH

UniProtKB: Pannexin-3

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
50.0 mMC4H11NO3Tris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3297870
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 393863
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: ModelAngelo model generated with the full-length amino acid sequences
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9kom:
Cryo-EM structure of human pannexin-3 protomer

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