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- EMDB-28902: Cryo-EM structure of human pannexin 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-28902
TitleCryo-EM structure of human pannexin 2
Map data
Sample
  • Organelle or cellular component: human pannexin 2
    • Protein or peptide: Pannexin-2, Soluble cytochrome b562 fusion
KeywordsIon channel / 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 / electron transport chain / cell-cell signaling / monoatomic ion transmembrane transport / periplasmic space ...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 / electron transport chain / cell-cell signaling / monoatomic ion transmembrane transport / periplasmic space / electron transfer activity / iron ion binding / Golgi membrane / heme binding / endoplasmic reticulum membrane / protein-containing complex binding / structural molecule activity / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Pannexin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsHe Z / Yuan P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS109307 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural and functional analysis of human pannexin 2 channel.
Authors: Zhihui He / Yonghui Zhao / Michael J Rau / James A J Fitzpatrick / Rajan Sah / Hongzhen Hu / Peng Yuan /
Abstract: The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of ...The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of PANX2 channel function remains largely unknown. Here, we present a cryo-electron microscopy structure of human PANX2, which reveals pore properties contrasting with those of the intensely studied paralog PANX1. The extracellular selectivity filter, defined by a ring of basic residues, more closely resembles that of the distantly related volume-regulated anion channel (VRAC) LRRC8A, rather than PANX1. Furthermore, we show that PANX2 displays a similar anion permeability sequence as VRAC, and that PANX2 channel activity is inhibited by a commonly used VRAC inhibitor, DCPIB. Thus, the shared channel properties between PANX2 and VRAC may complicate dissection of their cellular functions through pharmacological manipulation. Collectively, our structural and functional analysis provides a framework for development of PANX2-specific reagents that are needed for better understanding of channel physiology and pathophysiology.
History
DepositionNov 18, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28902.png

Downloads & links

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Map

FileDownload / File: emd_28902.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 280 pix.
= 252. Å		0.9 Å/pix.
x 280 pix.
= 252. Å		0.9 Å/pix.
x 280 pix.
= 252. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.86
Minimum - Maximum-2.8885088 - 5.437744
Average (Standard dev.)0.018787865 (±0.15435122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28902_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28902_half_map_2.map
Projections & Slices
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Sample components

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Entire : human pannexin 2

EntireName: human pannexin 2
Components
  • Organelle or cellular component: human pannexin 2
    • Protein or peptide: Pannexin-2, Soluble cytochrome b562 fusion

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Supramolecule #1: human pannexin 2

SupramoleculeName: human pannexin 2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Pannexin-2, Soluble cytochrome b562 fusion

MacromoleculeName: Pannexin-2, Soluble cytochrome b562 fusion / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 55.033406 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
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 ITNESDADLE DNWETLNDNL KVIEKADNAA QVKD ALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLSN SLEV LFQ

UniProtKB: Pannexin-2, Soluble cytochrome b562

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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

Concentration7.5 mg/mL
BufferpH: 8
Details: 20mM Tris-HCL, 150mM NaCl, 40uM GDN, 1mM Fluorinated Fos-Choline-8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm

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Image processing

Particle selectionNumber selected: 467552
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25191
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Avg.num./class: 16885 / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 78.73
Output model

PDB-8f7c:
Cryo-EM structure of human pannexin 2

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