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- EMDB-33273: Cryo-EM structure of human pannexin 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-33273
TitleCryo-EM structure of human pannexin 3
Map dataem map
Sample
  • Complex: Heptamer of human pannexin 3 channel
    • 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: 3.25 Å
AuthorsHang Z / Huawei Z / Daping W
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900046 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 human pannexin 3
Authors: Hang Z / Huawei Z / Daping W
History
DepositionApr 21, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33273.png

Downloads & links

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Map

FileDownload / File: emd_33273.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.8895929 - 2.9807327
Average (Standard dev.)0.0026584668 (±0.075243875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_33273_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_33273_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heptamer of human pannexin 3 channel

EntireName: Heptamer of human pannexin 3 channel
Components
  • Complex: Heptamer of human pannexin 3 channel
    • Protein or peptide: Pannexin-3

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Supramolecule #1: Heptamer of human pannexin 3 channel

SupramoleculeName: Heptamer of human pannexin 3 channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 312.78 MDa

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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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136536
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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