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- EMDB-49849: Structure of a pentameric Nanchung in complex with Afidopyropen -

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Basic information

Entry
Database: EMDB / ID: EMD-49849
TitleStructure of a pentameric Nanchung in complex with Afidopyropen
Map dataStructure of a pentameric Nanchung in complex with Afidopyropen
Sample
  • Complex: Nanchung
    • Protein or peptide: Nanchung
  • Ligand: Afidopyropen
KeywordsMembrane protein / membrane channel / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human) / Halyomorpha halys (brown marmorated stink bug)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsFedor JG / Lee S-Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS132231 United States
CitationJournal: Nat Commun / Year: 2025
Title: Visualizing insecticide control of insect TRP channel function and assembly.
Authors: Justin G Fedor / Ramani Kandasamy / Cheon-Gyu Park / Yang Suo / Martin Weisel / Nancy B Rankl / Alexandre Nesterov / Seok-Yong Lee /
Abstract: Insecticides are vital to combating world food shortages and transmission of vector-borne human diseases. Increasing insecticide resistance necessitates discovery of novel compounds against ...Insecticides are vital to combating world food shortages and transmission of vector-borne human diseases. Increasing insecticide resistance necessitates discovery of novel compounds against underutilized targets. Nanchung (Nan) and Inactive (Iav), the transient receptor potential vanilloid-type (TRPV) channels in insects, likely form a heteromeric channel (Nan-Iav) and are localized in mechanosensory chordotonal organs which confer gravitaxis, hearing and proprioception. Several insecticides, such as afidopyropen (AP), target Nan-Iav through unknown mechanisms. Effective against piercing-sucking (hemipteran) insects, AP disrupts chordotonal functions preventing feeding. AP can bind to Nan alone, but only Nan-Iav exhibits channel activity with agonists including endogenous nicotinamide (NAM). Despite its importance as an insecticide target, much is unknown about Nan-Iav, such as channel assembly, modulator binding sites, and Ca-dependent regulation, hampering further insecticide development. Here we present the cryo-electron microscopy structures of hemipteran Nan-Iav with calmodulin bound in the apo state and with AP and NAM bound to cytosolic ankyrin repeat domain (ARD) interfaces. Unexpectedly, we found that Nan alone can form a pentamer, stabilized through AP-mediated ARD interactions. Our study provides molecular insights into insecticide and agonist interactions with Nan-Iav, highlighting the importance of the ARD on channel function and assembly, while also probing regulation by Ca.
History
DepositionMar 21, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49849.png

Downloads & links

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Map

FileDownload / File: emd_49849.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a pentameric Nanchung in complex with Afidopyropen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7824992 - 3.2854803
Average (Standard dev.)0.0066785016 (±0.07258978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_49849_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_49849_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nanchung

EntireName: Nanchung
Components
  • Complex: Nanchung
    • Protein or peptide: Nanchung
  • Ligand: Afidopyropen

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Supramolecule #1: Nanchung

SupramoleculeName: Nanchung / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Nanchung

MacromoleculeName: Nanchung / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Halyomorpha halys (brown marmorated stink bug)
Molecular weightTheoretical: 104.941031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNTESNVTS GVKKQADTSS IKIYKLVDLK GGGLLVELMK RAAQTKQYAE LDHAIKTKVE PFLYNKGQGK MMPVSQLVLM RNKERPRHK MLPPLRNLEN PDDYDIESYV VPEPTEEDLK DPNKYREVCW DLKERGAVGE TILHLCLLNA TSLHADLAKR L LRFYPKLI ...String:
MGNTESNVTS GVKKQADTSS IKIYKLVDLK GGGLLVELMK RAAQTKQYAE LDHAIKTKVE PFLYNKGQGK MMPVSQLVLM RNKERPRHK MLPPLRNLEN PDDYDIESYV VPEPTEEDLK DPNKYREVCW DLKERGAVGE TILHLCLLNA TSLHADLAKR L LRFYPKLI NDVYMSDEYY GESVLHIAIV NEDPAMVKFL LDSGVNVNER CFGNFMCPED QKASRTDSFD HEWVNLQSFT TY EGYVYWG EYPLSFAACL GQEECYRLML ARGANPDNQD TNGNTVLHML VIYSKIQTFD MAYEVGGDLS IRNVQYLTPL TLA AKLARI ELFFHILNIE REIYWQIGSI TCAAYPLSQI DTIDIVTGNI SKNSALNLVV FGEKDEHLEL MDGVLIDLLN AKWN AFVKF RFYRQFFLFL FYFLISLICF TLRPGPPPVK PISSINSTKP NGNNITADLS PENLTTLPKW IYKTEIKKYD PEDNT SQNS RLNVILREVI LTSLKVEDID KVVSFSNAET PDNSREDAEG LVCNGNSIHS CIGNGSDVIS VFGKGKSPKV PKPGAS ADD FDYDDTWWEE FGQCRLLQVT SYIEMTRLIS EVMLDIGALL YILAALREAR FLGWSMFVEN LMTAPSRVMF LFSCCLM LT MPFLRFTCNE EIEDMMAVII MLTTAPYFLF FCRGFKTVGP FVVMIYRMIM GDLLRFATIY LVFVMGFAQA YYIIFLSF D NPLTPEGVDD SVSNPIPNPM EAVMAMFFMS MTSFGDYYPA LERTAHEFCA KLCFVIYMAI VAILLVNMLI AMMGNTYQK IAETRNEWQR QWARIVLVVE RGVSPSERLT KLMWYSQPMS DGRRALVLRL NQSEEDKEEM KEILEMKRIH NRMVQKRKER EMSTTKSPN LINLNSPIEN TKNKNPFSAN SLEVLFQ

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Macromolecule #2: Afidopyropen

MacromoleculeName: Afidopyropen / type: ligand / ID: 2 / Number of copies: 5 / Formula: A1B32
Molecular weightTheoretical: 593.664 Da

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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

Concentration2.9 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClNaCl
0.02 %GDNGDN
1.0 uMAPAfidopyropen
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 240 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00037 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse sample

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMax: 70.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6114 / Average exposure time: 2.4 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 729894
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 481923
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.0)

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Atomic model buiding 1

Initial modelPDB ID:

5wo7


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 112.4
Output model

PDB-9nvs:
Structure of a pentameric Nanchung in complex with Afidopyropen

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