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- EMDB-65644: ratTRPV1 bound with antagonist AMG9810 -

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Basic information

Entry
Database: EMDB / ID: EMD-65644
TitleratTRPV1 bound with antagonist AMG9810
Map data
Sample
  • Complex: ratTRPV1 bound with antagonist AMG9810
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
  • Ligand: (~{Z})-3-(4-~{tert}-butylphenyl)-~{N}-(2,3-dihydro-1,4-benzodioxin-6-yl)prop-2-enamide
  • Ligand: SODIUM ION
Keywordsantagonist / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain ...negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / positive regulation of renal sodium excretion / TRP channels / negative regulation of axon regeneration / positive regulation of cardiac muscle cell differentiation / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / thermoception / urinary bladder smooth muscle contraction / response to pH / glutamate secretion / monoatomic cation transmembrane transporter activity / negative regulation of systemic arterial blood pressure / excitatory extracellular ligand-gated monoatomic ion channel activity / dendritic spine membrane / negative regulation of heart rate / response to acidic pH / positive regulation of urine volume / response to pain / diet induced thermogenesis / cellular response to alkaloid / detection of maltose stimulus / temperature homeostasis / cellular response to cytokine stimulus / maltose transport complex / cellular response to ATP / intracellularly gated calcium channel activity / detection of temperature stimulus involved in sensory perception of pain / carbohydrate transport / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / behavioral response to pain / positive regulation of vasoconstriction / carbohydrate transmembrane transporter activity / maltose binding / monoatomic ion channel activity / maltose transport / maltodextrin transmembrane transport / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to acidic pH / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / ATP-binding cassette (ABC) transporter complex / sensory perception of pain / axon terminus / positive regulation of excitatory postsynaptic potential / sarcoplasmic reticulum / cell chemotaxis / lipid metabolic process / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to peptide hormone / cellular response to growth factor stimulus / GABA-ergic synapse / cellular response to tumor necrosis factor / calcium ion transmembrane transport / calcium channel activity / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / outer membrane-bounded periplasmic space / sensory perception of taste / response to heat / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / protein homotetramerization / calmodulin binding / periplasmic space / postsynaptic membrane / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / DNA damage response / dendrite / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / metal ion binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) ...Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsGao YH / Li ZX
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021ZD0203400 China
CitationJournal: Cell Rep / Year: 2026
Title: Structures of TRPV1 bound by hyperthermia-inducing analgesics.
Authors: Yu-Hao Gao / Yi-Zhe Huang / Zhao-Xing Li / Xiao-Ying Chen / Chang-Yan Shao / Han-Wen Li / Bin Liu / Fán Yang / Mei-Rong Chen / Mei-Ling Lu / Michael X Zhu / Fan Yang / Yi-Bei Xiao / Ye Yu /
Abstract: TRPV1, a member of the transient receptor potential vanilloid subfamily, mediates nociception and thermoregulation. TRPV1-targeting analgesics frequently induce hyperthermia, underscoring the need ...TRPV1, a member of the transient receptor potential vanilloid subfamily, mediates nociception and thermoregulation. TRPV1-targeting analgesics frequently induce hyperthermia, underscoring the need for structural insights to guide the development of safer compounds. Here, we determined the structures of rat TRPV1 bound to the clinical candidate analgesics AMG517, AMG9810, and SB366791. AMG517 and AMG9810 are deeply situated within the S3-S4 interface of the vanilloid pocket, where they interact with residues from the S3-S6 helices, as well as the S4-S5 linker. These interactions induce local deformations in the TRP-box and lower S6 helix, accompanied by a modest rotation of the S1-S4 bundle, leading to partial dilation of the lower gate. The distinct allosteric changes of AMG517 and AMG9810, compared with the non-hyperthermic ligand SB366791, suggest a structural basis by which TRPV1-targeting analgesics influence thermoregulation and provide insights for designing safer analogs.
History
DepositionAug 1, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65644.png

Downloads & links

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Map

FileDownload / File: emd_65644.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0932
Minimum - Maximum-0.001737758 - 1.894748
Average (Standard dev.)0.0023967673 (±0.031706374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_65644_additional_1.map
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Half map: #2

Fileemd_65644_half_map_1.map
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Half map: #1

Fileemd_65644_half_map_2.map
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Sample components

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Entire : ratTRPV1 bound with antagonist AMG9810

EntireName: ratTRPV1 bound with antagonist AMG9810
Components
  • Complex: ratTRPV1 bound with antagonist AMG9810
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
  • Ligand: (~{Z})-3-(4-~{tert}-butylphenyl)-~{N}-(2,3-dihydro-1,4-benzodioxin-6-yl)prop-2-enamide
  • Ligand: SODIUM ION

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Supramolecule #1: ratTRPV1 bound with antagonist AMG9810

SupramoleculeName: ratTRPV1 bound with antagonist AMG9810 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Transient recept...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 140.466562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNSGTGGGSG DDDDKSPMGS HHHHHHHHGS DYDI PTTEN LYFQGAMDPM EQRASLDSEE SESPPQENSC LDPPDRDPNC KPPPVKPHIF TTRSRTRLFG KGDSEEASPL DCPYE EGGL ASCPIITVSS VLTIQRPGDG PASVRPSSQD SVSAGEKPPR LYDRRSIFDA VAQSNCQELE SLLPFLQRSK KRLTDS EFK DPETGKTCLL KAMLNLHNGQ NDTIALLLDV ARKTDSLKQF VNASYTDSYY KGQTALHIAI ERRNMTLVTL LVENGAD VQ AAANGDFFKK TKGRPGFYFG ELPLSLAACT NQLAIVKFLL QNSWQPADIS ARDSVGNTVL HALVEVADNT VDNTKFVT S MYNEILILGA KLHPTLKLEE ITNRKGLTPL ALAASSGKIG VLAYILQREI HEPECRHLSR KFTEWAYGPV HSSLYDLSC IDTCEKNSVL EVIAYSSSET PNRHDMLLVE PLNRLLQDKW DRFVKRIFYF NFFVYCLYMI IFTAAAYYRP VEGLPPYKLK NTVGDYFRV TGEILSVSGG VYFFFRGIQY FLQRRPSLKS LFVDSYSEIL FFVQSLFMLV SVVLYFSQRK EYVASMVFSL A MGWTNMLY YTRGFQQMGI YAVMIEKMIL RDLCRFMFVY LVFLFGFSTA VVTLIEDGKN NSLPMESTPH KCRGSACKPG NS YNSLYST CLELFKFTIG MGDLEFTENY DFKAVFIILL LAYVILTYIL LLNMLIALMG ETVNKIAQES KNIWKLQRAI TIL DTEKSF LKCMRKAFRS GKLLQVGFTP DGKDDYRWCF RVDEVNWTTW NTNVGIINED PGNCEGVKRT LSFSLRSGRV SGRN WKNFA LVPLLRDAST RDRHATQQEE VQLKHYTGSL KPEDAEVFKD SMVPGEK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: (~{Z})-3-(4-~{tert}-butylphenyl)-~{N}-(2,3-dihydro-1,4-benzodioxi...

MacromoleculeName: (~{Z})-3-(4-~{tert}-butylphenyl)-~{N}-(2,3-dihydro-1,4-benzodioxin-6-yl)prop-2-enamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1D6W
Molecular weightTheoretical: 337.412 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 115503
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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