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- PDB-6m66: The Cryo-EM Structure of Human Pannexin 1 -

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Basic information

Entry
Database: PDB / ID: 6m66
TitleThe Cryo-EM Structure of Human Pannexin 1
ComponentsPannexin-1
KeywordsTRANSPORT PROTEIN / Pannexin 1 / ATP release / Heptameric channel
Function / homology
Function and homology information


ATP transmembrane transporter activity / ATP transport / leak channel activity / Electric Transmission Across Gap Junctions / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / gap junction / monoatomic anion channel activity ...ATP transmembrane transporter activity / ATP transport / leak channel activity / Electric Transmission Across Gap Junctions / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / gap junction / monoatomic anion channel activity / gap junction channel activity / positive regulation of macrophage cytokine production / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / oogenesis / response to ATP / The NLRP3 inflammasome / monoatomic cation transport / positive regulation of interleukin-1 beta production / response to ischemia / calcium channel activity / calcium ion transport / actin filament binding / cell-cell signaling / protease binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / scaffold protein binding / transmembrane transporter binding / signaling receptor binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJin, Q. / Bo, Z. / Xiang, Z. / Xiaokang, Z. / Ye, S.
CitationJournal: Cell Res / Year: 2020
Title: Cryo-EM structures of human pannexin 1 channel.
Authors: Qiuheng Jin / Bo Zhang / Xiang Zheng / Ningning Li / Lingyi Xu / Yuan Xie / Fangjun Song / Eijaz Ahmed Bhat / Yuan Chen / Ning Gao / Jiangtao Guo / Xiaokang Zhang / Sheng Ye /
History
DepositionMar 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Pannexin-1
B: Pannexin-1
C: Pannexin-1
D: Pannexin-1
E: Pannexin-1
F: Pannexin-1
G: Pannexin-1


Theoretical massNumber of molelcules
Total (without water)348,3457
Polymers348,3457
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23090 Å2
ΔGint-144 kcal/mol
Surface area96340 Å2

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Components

#1: Protein
Pannexin-1


Mass: 49763.574 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANX1, MRS1, UNQ2529/PRO6028 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q96RD7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pannexin 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pEG BacMam
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMHEPES1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 57.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3247: / Classification: refinement
EM software
IDNameVersionCategory
4cryoSPARC2CTF correction
8PHENIXmodel refinement
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145716 / Symmetry type: POINT

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