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- EMDB-65638: ratTRPV1 bound with antagonist AMG517 -

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Basic information

Entry
Database: EMDB / ID: EMD-65638
TitleratTRPV1 bound with antagonist AMG517
Map data
Sample
  • Complex: ratTRPV1 bound with antagonist AMG517
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
  • Ligand: ~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]ethanamide
  • Ligand: SODIUM ION
Keywordsantagonist / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / cellular response to temperature stimulus / peptide secretion / smooth muscle contraction involved in micturition / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels ...negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / cellular response to temperature stimulus / peptide secretion / smooth muscle contraction involved in micturition / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels / fever generation / detection of temperature stimulus involved in thermoception / urinary bladder smooth muscle contraction / thermoception / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / response to pH / chloride channel regulator activity / dendritic spine membrane / monoatomic cation transmembrane transporter activity / glutamate secretion / ligand-gated monoatomic ion channel activity / negative regulation of heart rate / response to pain / temperature homeostasis / diet induced thermogenesis / cellular response to alkaloid / detection of maltose stimulus / maltose transport complex / cellular response to ATP / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / intracellularly gated calcium channel activity / carbohydrate transport / behavioral response to pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / monoatomic cation channel activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to peptide hormone / calcium ion transmembrane transport / GABA-ergic synapse / lipid metabolic process / cellular response to growth factor stimulus / calcium channel activity / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / transmembrane signaling receptor activity / calcium ion transport / sensory perception of taste / cellular response to heat / outer membrane-bounded periplasmic space / positive regulation of cytosolic calcium ion concentration / response to heat / monoatomic ion transmembrane transport / protein homotetramerization / postsynaptic membrane / calmodulin binding / periplasmic space / 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 / metal ion binding / identical protein binding / membrane / 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 repeats (3 copies) / Ankyrin repeat profile. ...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 repeats (3 copies) / Ankyrin repeat profile. / 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: 2.7 Å
AuthorsGao YH / Li ZX
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021ZD0203400 China
CitationJournal: To Be Published
Title: ratTRPV1 bound with antagonist AMG517
Authors: Gao YH / Li ZX
History
DepositionJul 31, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65638.png

Downloads & links

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Map

FileDownload / File: emd_65638.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0913
Minimum - Maximum-0.002011685 - 1.5885043
Average (Standard dev.)0.0027064236 (±0.03389325)
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_65638_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65638_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65638_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ratTRPV1 bound with antagonist AMG517

EntireName: ratTRPV1 bound with antagonist AMG517
Components
  • Complex: ratTRPV1 bound with antagonist AMG517
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
  • Ligand: ~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]ethanamide
  • Ligand: SODIUM ION

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Supramolecule #1: ratTRPV1 bound with antagonist AMG517

SupramoleculeName: ratTRPV1 bound with antagonist AMG517 / 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: ~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benz...

MacromoleculeName: ~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]ethanamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1D6R
Molecular weightTheoretical: 430.403 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
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: 2.5 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 368794
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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