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- EMDB-61368: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-61368
TitleCryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1
Map data
Sample
  • Complex: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1
    • Protein or peptide: Pannexin-3
KeywordsATP channel / Calcium channel / heptamer / MEMBRANE 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: 3.7 Å
AuthorsZhang H / Zhang HW / Wang D
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900046 China
National Natural Science Foundation of China (NSFC)82302764 China
National Natural Science Foundation of China (NSFC)81972085 China
National Natural Science Foundation of China (NSFC)82172465 China
CitationJournal: To Be Published
Title: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1
Authors: Zhang H / Zhang HW / Wang D
History
DepositionAug 29, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61368.png

Downloads & links

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Map

FileDownload / File: emd_61368.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.)
0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.7536138 - 1.5098902
Average (Standard dev.)0.0046762237 (±0.04450936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61368_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61368_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 : Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1

EntireName: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1
Components
  • Complex: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1
    • Protein or peptide: Pannexin-3

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Supramolecule #1: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1

SupramoleculeName: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310 KDa

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Macromolecule #1: Pannexin-3

MacromoleculeName: Pannexin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.734219 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 ACDEHP

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

Concentration12 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris2-Amino-2-hydroxymethyl-1,3-propanediol
150.0 mMNaClsodium chloride
0.02 %GDNGlyco-diosgenin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102449
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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