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- EMDB-49845: Structure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide -

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Basic information

Entry
Database: EMDB / ID: EMD-49845
TitleStructure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide
Map dataStructure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide
Sample
  • Complex: Nanchung-Inactive-Calmodulin
    • Protein or peptide: Inactive
  • Protein or peptide: Nanchung
  • Protein or peptide: Calmodulin-1
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: NICOTINAMIDE
  • Ligand: CALCIUM ION
  • Ligand: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
KeywordsMembrane protein / membrane channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


cation channel complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase ...cation channel complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcium ion import across plasma membrane / RHO GTPases activate PAKs / regulation of ryanodine-sensitive calcium-release channel activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / cellular response to interferon-beta / Protein methylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / Ion homeostasis / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Stimuli-sensing channels / calcium channel activity / spindle pole / calcium-dependent protein binding / Signaling by RAF1 mutants / RAS processing / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / long-term synaptic potentiation / Platelet degranulation / sperm midpiece / myelin sheath / synaptic vesicle membrane / Inactivation, recovery and regulation of the phototransduction cascade / RAF/MAP kinase cascade / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / vesicle
Similarity search - Function
Transient receptor potential cation channel subfamily V / : / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif ...Transient receptor potential cation channel subfamily V / : / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Ion transport domain-containing protein / Uncharacterized protein / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Halyomorpha halys (brown marmorated stink bug)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 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_49845.png

Downloads & links

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Map

FileDownload / File: emd_49845.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2053378 - 2.2472353
Average (Standard dev.)0.002682077 (±0.058515638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_49845_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_49845_half_map_2.map
Annotationhalf map 2
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Nanchung-Inactive-Calmodulin

EntireName: Nanchung-Inactive-Calmodulin
Components
  • Complex: Nanchung-Inactive-Calmodulin
    • Protein or peptide: Inactive
  • Protein or peptide: Nanchung
  • Protein or peptide: Calmodulin-1
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: NICOTINAMIDE
  • Ligand: CALCIUM ION
  • Ligand: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid

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Supramolecule #1: Nanchung-Inactive-Calmodulin

SupramoleculeName: Nanchung-Inactive-Calmodulin / 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: Inactive

MacromoleculeName: Inactive / type: protein_or_peptide / ID: 1
Details: The 30-N-terminal residues are MGIIWGSGASSVNAGTVLDRVISQASNKDE. The authors were not able to assign the register of the residues in this region
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Halyomorpha halys (brown marmorated stink bug)
Molecular weightTheoretical: 109.381992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)CLLYKLANY K KGGELIDA YNAGGQSEVE ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)CLLYKLANY K KGGELIDA YNAGGQSEVE KLIREQFGQL MYNEGKGALI NRAEYLRWKF RDMQQVQIPI EASLSSQDPL SKWEDHQACW QM QYRGSLG ETLLHVLIIC DTKIHTRLAR TLLKCFPNLA IDVVEGEEYL GASALHLAIA YFNNELVQDL VEAGANVEQR AIG SFFLPR DQQGQRPSKH TDYEGLAYLG EYPLAWAACC ANESIYNLLL DNGANPDQRD TFGNMILHMV VVCDKLDMFG YALR HPKMP ASNGIANVAG LTPLTLACKL GRAKVFREML ELSAREFWRY SNITCSAYPL NALDTLLPDG RTNWNSALFI ILNGT KEEH LDMLDGGIIQ RLLEEKWKTF ARRQFLKRLV ILMLHLICLS GAVYLRPTDR TKPLLGGDDW KSIARQGFEV ATVLGV LSY VLVQQGGEIR NQGFISFIKQ LDPAKAIFLV SNILILVCIP FRLIDDKRTE EAILVFAVPG SWFLLMFFAG AVRLTGP FV TMVYSMIVGD MFTFGIIYSI VLFGFSQSFY FLYKGFPGVK NTLYSSYHST WMALFQITLG DYNYAELSHT SYPTLSKT V FAIFMVLVPI LLLNMLIAMM GNTYAHVIEQ SEKEWMKQWA KIVVSLERAV NQEDCKQYLQ EYSIKLGPGD DPSTEQRGV MVIKSKSKTR AKQRKGAVAN WKRVGKVTIN ELRKRGMNGE QLRRIMWDRA SISTPVKVPQ NPVVDVLMEN TAEQQAQQTP GSFGGALTA ALDVMAFTHD LDLSASGITS SGLNAKELIV SDPFRDLVLS SEIDVGEEEL ATLAEAAVLS VMSGQSDESE K LKIAKFNK QISFEQNAVL EVSDSDGFLD GQPLGQGSRA RKVKSAQERQ RAERTWGGTS ISSIEEPPPY LPLPPPPPLH SH QRPRPKT AKPNRVVPEA VVAKRPQSSA LGDRVKSPPE LLEPWSTRGI ATINTILAWQ PSDQDSM

UniProtKB: Uncharacterized protein, Ion transport domain-containing protein

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Macromolecule #2: Nanchung

MacromoleculeName: Nanchung / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Halyomorpha halys (brown marmorated stink bug)
Molecular weightTheoretical: 101.194867 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 EM

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Macromolecule #3: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.167979 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMA

UniProtKB: Calmodulin-1

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Macromolecule #4: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 14 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 6 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #6: NICOTINAMIDE

MacromoleculeName: NICOTINAMIDE / type: ligand / ID: 6 / Number of copies: 2 / Formula: NCA
Molecular weightTheoretical: 122.125 Da
Chemical component information

ChemComp-NCA:
NICOTINAMIDE / medication*YM

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-...

MacromoleculeName: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
type: ligand / ID: 8 / Number of copies: 2 / Formula: D39
Molecular weightTheoretical: 762.006 Da
Chemical component information

ChemComp-D39:
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid

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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

Concentration1.9 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClNaCl
0.02 %GDNGDN
5.0 %glycerolglycerol
1.0 mMNAMNicotinamide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 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: 11850 / 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: 4721956
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: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 226876
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: 60
Output model

PDB-9nvo:
Structure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide

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