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- PDB-9jct: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 2 -

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Basic information

Entry
Database: PDB / ID: 9jct
TitleCryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 2
ComponentsPannexin-3
KeywordsMEMBRANE PROTEIN / ATP channel / Calcium channel / heptamer
Function / homology
Function and homology information


gap junction hemi-channel activity / wide pore channel activity / positive regulation of interleukin-1 production / gap junction / monoatomic cation transport / calcium channel activity / osteoblast differentiation / cell-cell signaling / endoplasmic reticulum membrane / 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: 4.5 Å
AuthorsZhang, H. / Zhang, H. / Wang, D.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900046 China
National Natural Science Foundation of China (NSFC)82302764 China
National Natural Science Foundation of China (NSFC)81972085 China
National Natural Science Foundation of China (NSFC)82172465 China
CitationJournal: To Be Published
Title: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 2
Authors: Zhang, H. / Zhang, H. / Wang, D.
History
DepositionAug 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pannexin-3
B: Pannexin-3
C: Pannexin-3
D: Pannexin-3
E: Pannexin-3
F: Pannexin-3
G: Pannexin-3


Theoretical massNumber of molelcules
Total (without water)313,1407
Polymers313,1407
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "A"
d_7ens_1chain "G"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 377 / Label seq-ID: 2 - 377

Dom-IDAuth asym-IDLabel asym-ID
d_1FF
d_2BB
d_3CC
d_4DD
d_5EE
d_6AA
d_7GG

NCS oper:
IDCodeMatrixVector
1given(-0.715607526323, 0.655260812725, -0.241948621769), (0.368289082297, 0.648273076941, 0.666412161934), (0.593522552335, 0.387782522839, -0.705234496356)176.803526305, -92.7136947595, 98.35477088
2given(-0.705251154768, 0.378570126775, 0.599420943755), (0.671743964883, 0.627152176133, 0.394259043796), (-0.226673453104, 0.680709047306, -0.696601994379)100.629831837, -94.7751427291, 170.050876727
3given(-0.10464098907, 0.085467925963, 0.990830710585), (0.645426954248, 0.763818605426, 0.0022770013314), (-0.756620320991, 0.63974711538, -0.135090037482)5.78969017499, -57.4888529942, 169.39453528
4given(0.669320207855, -0.141096951649, 0.729453295004), (0.336940230978, 0.932680439652, -0.128757439549), (-0.662179537667, 0.331962117908, 0.671803105209)-35.1595499327, -18.8833264651, 90.1805355035
5given(-0.0863135862367, 0.611819435056, -0.786274089436), (0.0294699497085, 0.790442023996, 0.611827531879), (0.995832057576, 0.029637570562, -0.0862561737851)170.617396539, -59.2681678017, 8.240186083
6given(0.648486386242, 0.359812037898, -0.670820918161), (-0.129662576666, 0.920570402822, 0.368426043678), (0.750102008443, -0.151938904932, 0.643631529757)90.3190780326, -20.8692297702, -33.9530235922

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Components

#1: Protein
Pannexin-3


Mass: 44734.219 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANX3 / Production host: Homo sapiens (human) / References: UniProt: Q96QZ0
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: Cryo-EM structure of asymmetric pannexin 3 heptamer in GDN class 2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.31 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-Amino-2-hydroxymethyl-1,3-propanediolTris1
2150 mMsodium chlorideNaCl1
30.02 %Glyco-diosgeninGDN1
SpecimenConc.: 12 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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63958 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 270.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003120692
ELECTRON MICROSCOPYf_angle_d0.934228077
ELECTRON MICROSCOPYf_chiral_restr0.04373311
ELECTRON MICROSCOPYf_plane_restr0.00413416
ELECTRON MICROSCOPYf_dihedral_angle_d4.89862702
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FFELECTRON MICROSCOPYNCS constraints1.8241997901E-10
ens_1d_3FFELECTRON MICROSCOPYNCS constraints5.17110459969E-13
ens_1d_4FFELECTRON MICROSCOPYNCS constraints5.57457596254E-11
ens_1d_5FFELECTRON MICROSCOPYNCS constraints4.16015177744E-12
ens_1d_6FFELECTRON MICROSCOPYNCS constraints6.38600904406E-13
ens_1d_7FFELECTRON MICROSCOPYNCS constraints8.64002500912E-11

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