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- PDB-9w4m: ratTRPV1 bound with antagonist AMG517 -

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Basic information

Entry
Database: PDB / ID: 9w4m
TitleratTRPV1 bound with antagonist AMG517
ComponentsMaltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
KeywordsMEMBRANE PROTEIN / antagonist / complex
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 speciesEscherichia coli K-12 (bacteria)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGao, Y.H. / Li, Z.X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021ZD0203400 China
CitationJournal: To Be Published
Title: ratTRPV1 bound with antagonist AMG517
Authors: Gao, Y.H. / Li, Z.X.
History
DepositionJul 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
B: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
C: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
D: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)563,63410
Polymers561,8664
Non-polymers1,7686
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpV1 / Capsaicin receptor / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid receptor type 1-like


Mass: 140466.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: malE, b4034, JW3994, Trpv1, Vr1, Vr1l / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: O35433
#2: Chemical
ChemComp-A1D6R / ~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]ethanamide / AMG-517


Mass: 430.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H13F3N4O2S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ratTRPV1 bound with antagonist AMG517 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 368794 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00717972
ELECTRON MICROSCOPYf_angle_d0.76124340
ELECTRON MICROSCOPYf_dihedral_angle_d6.5122376
ELECTRON MICROSCOPYf_chiral_restr0.042712
ELECTRON MICROSCOPYf_plane_restr0.0083012

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