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- EMDB-33276: Cryo-EM structure of human pannexin 2 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33276
TitleCryo-EM structure of human pannexin 2
Map data
Sample
  • Complex: Heptamer of human pannexin 2 channel
    • Protein or peptide: Pannexin-2
KeywordsATP channel / Calcium channel / heptamer / MEMBRANE PROTEIN
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / gap junction channel activity / monoatomic cation transport / response to ischemia / cell-cell signaling / monoatomic ion transmembrane transport / Golgi membrane / endoplasmic reticulum membrane ...Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / gap junction channel activity / monoatomic cation transport / response to ischemia / cell-cell signaling / monoatomic ion transmembrane transport / Golgi membrane / endoplasmic reticulum membrane / protein-containing complex binding / 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: 3.44 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: Nat Commun / Year: 2023
Title: Cryo-EM structure of human heptameric pannexin 2 channel
Authors: Zhang H / Wang S / Zhang Z / Hou M / Du C / Zhao Z / Vogel H / Li Z / Yan K / Zhang X / Lu J / Liang Y / Yuan S / Wang D / Zhang H
History
DepositionApr 21, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33276.png

Downloads & links

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Map

FileDownload / File: emd_33276.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 264.96 Å		0.92 Å/pix.
x 288 pix.
= 264.96 Å		0.92 Å/pix.
x 288 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.9272999 - 3.6883218
Average (Standard dev.)0.007463098 (±0.08841167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33276_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33276_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 : Heptamer of human pannexin 2 channel

EntireName: Heptamer of human pannexin 2 channel
Components
  • Complex: Heptamer of human pannexin 2 channel
    • Protein or peptide: Pannexin-2

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Supramolecule #1: Heptamer of human pannexin 2 channel

SupramoleculeName: Heptamer of human pannexin 2 channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 323 KDa

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Macromolecule #1: Pannexin-2

MacromoleculeName: Pannexin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.301543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHLLEQSAD MATALLAGEK LRELILPGAQ DDKAGALAAL LLQLKLELPF DRVVTIGTVL VPILLVTLVF TKNFAEEPIY CYTPHNFTR DQALYARGYC WTELRDALPG VDASLWPSLF EHKFLPYALL AFAAIMYVPA LGWEFLASTR LTSELNFLLQ E IDNCYHRA ...String:
MHHLLEQSAD MATALLAGEK LRELILPGAQ DDKAGALAAL LLQLKLELPF DRVVTIGTVL VPILLVTLVF TKNFAEEPIY CYTPHNFTR DQALYARGYC WTELRDALPG VDASLWPSLF EHKFLPYALL AFAAIMYVPA LGWEFLASTR LTSELNFLLQ E IDNCYHRA AEGRAPKIEK QIQSKGPGIT EREKREIIEN AEKEKSPEQN LFEKYLERRG RSNFLAKLYL ARHVLILLLS AV PISYLCT YYATQKQNEF TCALGASPDG AAGAGPAVRV SCKLPSVQLQ RIIAGVDIVL LCVMNLIILV NLIHLFIFRK SNF IFDKLH KVGIKTRRQW RRSQFCDINI LAMFCNENRD HIKSLNRLDF ITNESDLMYD NVVRQLLAAL AQSNHDATPT VRDS GVQTV DPSAN

UniProtKB: Pannexin-2

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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

Concentration10 mg/mL
BufferpH: 7.6
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 K3 (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: 2.5 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: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108265
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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