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- EMDB-34376: Cryo-EM structure of human Pannexin-2 in pre-open state -

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Basic information

Entry
Database: EMDB / ID: EMD-34376
TitleCryo-EM structure of human Pannexin-2 in pre-open state
Map data
Sample
  • Complex: Pannexin-2
    • Protein or peptide: Pannexin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPannexin / ATP / Inner channel lipids / Cell-cell communication / 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: 3.4 Å
AuthorsCong Y / Jin X / Kong F / Yan C
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: To Be Published
Title: Inner channel lipids regulated gating mechanism of human pannexins.
Authors: Cong Y / Jin X / Kong F / Yan C
History
DepositionSep 23, 2022-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34376.png

Downloads & links

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Map

FileDownload / File: emd_34376.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-2.1639738 - 3.8989239
Average (Standard dev.)0.0064459452 (±0.08755336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34376_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34376_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34376_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Pannexin-2

EntireName: Pannexin-2
Components
  • Complex: Pannexin-2
    • Protein or peptide: Pannexin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Pannexin-2

SupramoleculeName: Pannexin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 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: 74.54193 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 DPSANPAEPD GAAEPPVVKR PRKKMKWIPT SNPLPQPFKE PLAIMRVENS KAEKPKPARR KTATDTLIAP LLDRS AHHY KGGGGDPGPG PAPAPAPPPA PDKKHARHFS LDVHPYILGT KKAKAEAVPA ALPASRSQEG GFLSQAEDCG LGLAPA PIK DAPLPEKEIP YPTEPARAGL PSGGPFHVRS PPAAPAVAPL TPASLGKAEP LTILSRNATH PLLHINTLYE AREEEDG GP RLPQDVGDLI AIPAPQQILI ATFDEPRTVV STVEF

UniProtKB: Pannexin-2

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration1.8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131444
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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