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- PDB-9pzo: heterotrimeric ENaC channel complex PPK1/PPK26/PPK26 with Vulnusin -

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Basic information

Entry
Database: PDB / ID: 9pzo
Titleheterotrimeric ENaC channel complex PPK1/PPK26/PPK26 with Vulnusin
Components
  • Amiloride-sensitive Na+ channel
  • Pickpocket 26
  • Vulnusin
KeywordsNEUROPEPTIDE / PPK / ENaC / ASIC / ion channel / ligand / Vulnusin / Nociception / nociceptor
Function / homology
Function and homology information


proprioception / larval locomotory behavior / pH-gated monoatomic ion channel activity / mechanosensory behavior / detection of chemical stimulus involved in sensory perception of pain / sodium ion transport / negative regulation of feeding behavior / monoatomic ion channel complex / ligand-gated monoatomic cation channel activity / behavioral response to pain ...proprioception / larval locomotory behavior / pH-gated monoatomic ion channel activity / mechanosensory behavior / detection of chemical stimulus involved in sensory perception of pain / sodium ion transport / negative regulation of feeding behavior / monoatomic ion channel complex / ligand-gated monoatomic cation channel activity / behavioral response to pain / sodium channel activity / detection of temperature stimulus involved in sensory perception of pain / detection of mechanical stimulus involved in sensory perception of pain / dendrite membrane / sodium ion transmembrane transport / membrane / plasma membrane
Similarity search - Function
Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
AMMONIUM ION / Pickpocket / Pickpocket 26
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJin, P. / Koepping, L. / Feng, S.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD026926 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021741 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD026881 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS122110 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097227 United States
CitationJournal: To Be Published
Title: Conformational changes of a Drosophila heterotrimeric ENaC channel complex PPK1/PPK26 triggered by binding of its ligand, the endogenous wound signal peptide Vulnusin
Authors: Jin, P. / Guo, Y. / Koepping, L. / Jan, L. / Jan, Y.N. / Feng, S.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amiloride-sensitive Na+ channel
D: Vulnusin
B: Pickpocket 26
C: Pickpocket 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,37313
Polymers206,2454
Non-polymers3,1289
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Amiloride-sensitive Na+ channel / FI02125p / Pickpocket


Mass: 69465.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: ppk, BG:DS06238.1, dfr, dmdNaC1, dmdNaCl, Dmel\CG3478, mdNaC1, pkt, PPK, Ppk, PPK1, ppk1, CG3478, Dmel_CG3478
Production host: Homo sapiens (human) / References: UniProt: Q7KT94
#3: Protein Pickpocket 26


Mass: 67932.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: ppk26, bba, Dmel\CG8546, PPK26, Ppk26, CG8546, Dmel_CG8546
Production host: Homo sapiens (human) / References: UniProt: Q9VS73

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Protein/peptide / Non-polymers , 2 types, 2 molecules D

#2: Protein/peptide Vulnusin


Mass: 915.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Homo sapiens (human)
#7: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N

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Sugars , 3 types, 8 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
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

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Details

Has ligand of interestN
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: PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin
Type: COMPLEX / Entity ID: #1, #3 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 31323126
3D reconstructionResolution: 2.86 Å
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11AF-Q7KT94-F1-v41AlphaFoldin silico model
21AF-Q9VS73-F1-v42AlphaFoldin silico model
RefinementHighest resolution: 2.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411593
ELECTRON MICROSCOPYf_angle_d0.61915725
ELECTRON MICROSCOPYf_dihedral_angle_d12.6444465
ELECTRON MICROSCOPYf_chiral_restr0.0441761
ELECTRON MICROSCOPYf_plane_restr0.0062037

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