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- EMDB-72074: heterotrimeric ENaC channel complex PPK1/PPK26/PPK26 with Vulnusin -

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Basic information

Entry
Database: EMDB / ID: EMD-72074
Titleheterotrimeric ENaC channel complex PPK1/PPK26/PPK26 with Vulnusin
Map dataheterotrimeric ENaC channel complex PPK1/PPK26/PPK26 with Vulnusin
Sample
  • Complex: PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin
    • Protein or peptide: Amiloride-sensitive Na+ channel
    • Protein or peptide: Pickpocket 26
  • Protein or peptide: Vulnusin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: AMMONIUM ION
KeywordsPPK / ENaC / ASIC / ion channel / ligand / Vulnusin / Nociception / nociceptor / NEUROPEPTIDE
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
Pickpocket / Pickpocket 26
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJin P / Koepping L / Feng S
Funding support United States, 6 items
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 YN / Feng S
History
DepositionAug 11, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72074.png

Downloads & links

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Map

FileDownload / File: emd_72074.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationheterotrimeric ENaC channel complex PPK1/PPK26/PPK26 with Vulnusin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 335.36 Å		1.05 Å/pix.
x 320 pix.
= 335.36 Å		1.05 Å/pix.
x 320 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-0.43459693 - 0.93908894
Average (Standard dev.)-0.00055277435 (±0.02204819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_72074_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72074_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin

EntireName: PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin
Components
  • Complex: PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin
    • Protein or peptide: Amiloride-sensitive Na+ channel
    • Protein or peptide: Pickpocket 26
  • Protein or peptide: Vulnusin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: AMMONIUM ION

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Supramolecule #1: PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin

SupramoleculeName: PPK1/PPK26/PPK26-heterotrimer in complex with Vulnusin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Amiloride-sensitive Na+ channel

MacromoleculeName: Amiloride-sensitive Na+ channel / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 69.465797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEIREDEEE KKSGISILPG PELLALPGFD TRASIASAAL SDVPSDVIIK SRIRYGSPLS ACKGLLLEYA KSTTIHGIRY IFEVHRPIY EKLYWLFFTC ISVYFAVSLI WDTYLKWQES PVILGFDETL VPVHKIPFPT ITICPEIKME RNVFDYTNVS R QLWEEYKQ ...String:
MAEIREDEEE KKSGISILPG PELLALPGFD TRASIASAAL SDVPSDVIIK SRIRYGSPLS ACKGLLLEYA KSTTIHGIRY IFEVHRPIY EKLYWLFFTC ISVYFAVSLI WDTYLKWQES PVILGFDETL VPVHKIPFPT ITICPEIKME RNVFDYTNVS R QLWEEYKQ NGNISDLDDE DLARMAVAMH ICDSEVVQRF TPLLSQLNPP NVDVTQTLID LSISKNETGP FCKWNGRFYF CD KIFDFVA TDEGICYQFN GLRPKDIYRD EKFISYVDPD VVDFNKYFDV DLPPWNNITG NWSLDTGFVD QGQNAYPQRT VFS SVKNGF FAFLQGLQHN FDYDCRSFKQ GYKVFLNSPE SVPLTTGNYI LVPHGDEVLV SVLPAYVVST DNLHEITPEK RQCL FDDER SLRFFRSYSQ SNCQTECLAN YTVSKCGCAK FWMPKPLGTP VCGLKDINCY TSAQDELYTL MQNQTMAKSI DESVD ITCN CMPACTSLEY NFEISRAKYD VAKTIRAFRE EYEHTDAIGS RLSVYFKEHQ FTAIKRTILF GVSTLISNCG GICGLF MGI SCLSFLELIY FFCMRICGSC RDRRKHKIQQ QNSVDLPEEK SEN

UniProtKB: Pickpocket

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Macromolecule #2: Vulnusin

MacromoleculeName: Vulnusin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 915.066 Da
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LSPGALKSAA

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Macromolecule #3: Pickpocket 26

MacromoleculeName: Pickpocket 26 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 67.932219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTDSTQPHT PSHEVAVRPP PCAANQWKRA ALMARMAPAF RETVSDDSED EVDTKKQIKY GSGFQAAKAI IHEYCDYTTI HGIRYLGEK KRPLLERLFW ISVLVLSVFT CVKLTLNIWD KWNNNPVIVS FAEKSTPVWQ IPFPAVTVCP ETKTRREIFN F TDSYHQVR ...String:
MSTDSTQPHT PSHEVAVRPP PCAANQWKRA ALMARMAPAF RETVSDDSED EVDTKKQIKY GSGFQAAKAI IHEYCDYTTI HGIRYLGEK KRPLLERLFW ISVLVLSVFT CVKLTLNIWD KWNNNPVIVS FAEKSTPVWQ IPFPAVTVCP ETKTRREIFN F TDSYHQVR DFQSNVSGIV DLSDKQKGLY GAVSQVCEPH LHDVTLGNKT RRGMEIIDAL TEVSPHFDDT YLNCKWRNSP VK CSDIFHK FVTEDGVCFS FNSLSPAEIF RAEGIIPDFI FREENRLSMD WNVEDGYSAS ADTSPYPNRV LGPGARAGLY LFM GGAEID FDDMCRGPVQ GFKILLHTPG DVAQVSKQYF RIPFDQEVLI SIRPKIITTS DGLKHYEPNR RQCYFQKERE LRYF NIYSQ SNCELECLAN FTLTKCGCVK FSMPRNVNMP VCGDASLKCY NQAEDELLLR EFTQGLVNAG ENTRGETECN CLPSC TSIA YEAEISQADF DYKTVINTDS PEGKEEQSKR QGMKMSRVSI FFKEAQFLTS RRSELYGTTD FLANCGGLLG LFMGVS MLS IVELIYFCTV RLISNLRMRR KTRKELLKAV NKDA

UniProtKB: Pickpocket 26

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: AMMONIUM ION

MacromoleculeName: AMMONIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: NH4
Molecular weightTheoretical: 18.038 Da
Chemical component information

ChemComp-NH4:
AMMONIUM ION

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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

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 31323126
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1-v4

source_name: AlphaFold, initial_model_type: in silico model

1-v4

source_name: AlphaFold, initial_model_type: in silico model
Output model

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

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