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- PDB-8gyq: Cryo-EM structure of human Pannexin-2 in pre-open state. -

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Basic information

Entry
Database: PDB / ID: 8gyq
TitleCryo-EM structure of human Pannexin-2 in pre-open state.
ComponentsPannexin-2
KeywordsMEMBRANE PROTEIN / Pannexin / ATP / Inner channel lipids / Cell-cell communication
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCong, Y. / Jin, X. / Kong, F. / Yan, C.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 17, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pannexin-2
B: Pannexin-2
C: Pannexin-2
D: Pannexin-2
E: Pannexin-2
F: Pannexin-2
G: Pannexin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,34214
Polymers521,7947
Non-polymers1,5487
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Pannexin-2


Mass: 74541.930 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANX2 / Production host: Homo sapiens (human) / References: UniProt: Q96RD6
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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-2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.500 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131444 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00720132
ELECTRON MICROSCOPYf_angle_d0.65627272
ELECTRON MICROSCOPYf_dihedral_angle_d4.752702
ELECTRON MICROSCOPYf_chiral_restr0.0363115
ELECTRON MICROSCOPYf_plane_restr0.0073458

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