3J5P

Structure of TRPV1 ion channel determined by single particle electron cryo-microscopy

> Summary

Summary for 3J5P

Related3J5Q 3J5R
EMDB informationEMD-5778 EMD-5776 EMD-5777
DescriptorTransient receptor potential cation channel subfamily V member 1
Functional Keywordstrpv1 channel, transport protein
Biological sourceRattus norvegicus (rat)
Total number of polymer chains4
Total molecular weight272971.34
Authors
Liao, M.,Cao, E.,Julius, D.,Cheng, Y. (deposition date: 2013-10-28, release date: 2013-12-04, Last modification date: 2013-12-18)
Primary citation
Liao, M.,Cao, E.,Julius, D.,Cheng, Y.
Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
Nature, 504:107-112, 2013
PubMed: 24305160
DOI: 10.1038/nature12822
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
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Structure validation

ClashscoreRamachandran outliersSidechain outliers78027.2%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 3j5p
no rotation
Molmil generated image of 3j5p
rotated about x axis by 90°
Molmil generated image of 3j5p
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
B, A, C, DTransient receptor potential cation channel subfamily V member 1polymer59868242.84
UniProt (O35433)
Rattus norvegicus (rat)@PDBjTrpV1, Capsaicin receptor, Osm-9-like TRP channel 1, OTRPC1, Vanilloid receptor 1, Vanilloid receptor type 1-like

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight272971.3
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight272971.3
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0030054cellular_componentcell junction
A0005829cellular_componentcytosol
A0030425cellular_componentdendrite
A0032591cellular_componentdendritic spine membrane
A0009897cellular_componentexternal side of plasma membrane
A0016021cellular_componentintegral component of membrane
A0005887cellular_componentintegral component of plasma membrane
A0031226cellular_componentintrinsic component of plasma membrane
A0016020cellular_componentmembrane
A0043025cellular_componentneuronal cell body
A0005886cellular_componentplasma membrane
A0045211cellular_componentpostsynaptic membrane
A0045202cellular_componentsynapse
A0005524molecular_functionATP binding
A0015278molecular_functioncalcium-release channel activity
A0005516molecular_functioncalmodulin binding
A0005261molecular_functioncation channel activity
A0008324molecular_functioncation transmembrane transporter activity
A0017081molecular_functionchloride channel regulator activity
A0005231molecular_functionexcitatory extracellular ligand-gated ion channel activity
A0005230molecular_functionextracellular ligand-gated ion channel activity
A0042802molecular_functionidentical protein binding
A0015276molecular_functionligand-gated ion channel activity
A0046872molecular_functionmetal ion binding
A0035091molecular_functionphosphatidylinositol binding
A0051219molecular_functionphosphoprotein binding
A0097603molecular_functiontemperature-gated ion channel activity
A0004888molecular_functiontransmembrane signaling receptor activity
A0048266biological_processbehavioral response to pain
A1990035
A0070588biological_processcalcium ion transmembrane transport
A0006816biological_processcalcium ion transport
A0071468biological_processcellular response to acidic pH
A0071312biological_processcellular response to alkaloid
A0071318biological_processcellular response to ATP
A0071345biological_processcellular response to cytokine stimulus
A0071363biological_processcellular response to growth factor stimulus
A0034605biological_processcellular response to heat
A1990090biological_processcellular response to nerve growth factor stimulus
A0071502biological_processcellular response to temperature stimulus
A0071356biological_processcellular response to tumor necrosis factor
A0050968biological_processdetection of chemical stimulus involved in sensory perception of pain
A0050965biological_processdetection of temperature stimulus involved in sensory perception of pain
A0050960biological_processdetection of temperature stimulus involved in thermoception
A0002024biological_processdiet induced thermogenesis
A0001660biological_processfever generation
A0014047biological_processglutamate secretion
A0006954biological_processinflammatory response
A0006629biological_processlipid metabolic process
A0001774biological_processmicroglial cell activation
A0090212biological_processnegative regulation of establishment of blood-brain barrier
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0002790biological_processpeptide secretion
A0043065biological_processpositive regulation of apoptotic process
A0007204biological_processpositive regulation of cytosolic calcium ion concentration
A0060454biological_processpositive regulation of gastric acid secretion
A0045429biological_processpositive regulation of nitric oxide biosynthetic process
A0051289biological_processprotein homotetramerization
A1901594biological_processresponse to capsazepine
A0009408biological_processresponse to heat
A0043434biological_processresponse to peptide hormone
A0009268biological_processresponse to pH
A0050954biological_processsensory perception of mechanical stimulus
A0060083biological_processsmooth muscle contraction involved in micturition
B0030054cellular_componentcell junction
B0005829cellular_componentcytosol
B0030425cellular_componentdendrite
B0032591cellular_componentdendritic spine membrane
B0009897cellular_componentexternal side of plasma membrane
B0016021cellular_componentintegral component of membrane
B0005887cellular_componentintegral component of plasma membrane
B0031226cellular_componentintrinsic component of plasma membrane
B0016020cellular_componentmembrane
B0043025cellular_componentneuronal cell body
B0005886cellular_componentplasma membrane
B0045211cellular_componentpostsynaptic membrane
B0045202cellular_componentsynapse
B0005524molecular_functionATP binding
B0015278molecular_functioncalcium-release channel activity
B0005516molecular_functioncalmodulin binding
B0005261molecular_functioncation channel activity
B0008324molecular_functioncation transmembrane transporter activity
B0017081molecular_functionchloride channel regulator activity
B0005231molecular_functionexcitatory extracellular ligand-gated ion channel activity
B0005230molecular_functionextracellular ligand-gated ion channel activity
B0042802molecular_functionidentical protein binding
B0015276molecular_functionligand-gated ion channel activity
B0046872molecular_functionmetal ion binding
B0035091molecular_functionphosphatidylinositol binding
B0051219molecular_functionphosphoprotein binding
B0097603molecular_functiontemperature-gated ion channel activity
B0004888molecular_functiontransmembrane signaling receptor activity
B0048266biological_processbehavioral response to pain
B1990035
B0070588biological_processcalcium ion transmembrane transport
B0006816biological_processcalcium ion transport
B0071468biological_processcellular response to acidic pH
B0071312biological_processcellular response to alkaloid
B0071318biological_processcellular response to ATP
B0071345biological_processcellular response to cytokine stimulus
B0071363biological_processcellular response to growth factor stimulus
B0034605biological_processcellular response to heat
B1990090biological_processcellular response to nerve growth factor stimulus
B0071502biological_processcellular response to temperature stimulus
B0071356biological_processcellular response to tumor necrosis factor
B0050968biological_processdetection of chemical stimulus involved in sensory perception of pain
B0050965biological_processdetection of temperature stimulus involved in sensory perception of pain
B0050960biological_processdetection of temperature stimulus involved in thermoception
B0002024biological_processdiet induced thermogenesis
B0001660biological_processfever generation
B0014047biological_processglutamate secretion
B0006954biological_processinflammatory response
B0006629biological_processlipid metabolic process
B0001774biological_processmicroglial cell activation
B0090212biological_processnegative regulation of establishment of blood-brain barrier
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0002790biological_processpeptide secretion
B0043065biological_processpositive regulation of apoptotic process
B0007204biological_processpositive regulation of cytosolic calcium ion concentration
B0060454biological_processpositive regulation of gastric acid secretion
B0045429biological_processpositive regulation of nitric oxide biosynthetic process
B0051289biological_processprotein homotetramerization
B1901594biological_processresponse to capsazepine
B0009408biological_processresponse to heat
B0043434biological_processresponse to peptide hormone
B0009268biological_processresponse to pH
B0050954biological_processsensory perception of mechanical stimulus
B0060083biological_processsmooth muscle contraction involved in micturition
C0030054cellular_componentcell junction
C0005829cellular_componentcytosol
C0030425cellular_componentdendrite
C0032591cellular_componentdendritic spine membrane
C0009897cellular_componentexternal side of plasma membrane
C0016021cellular_componentintegral component of membrane
C0005887cellular_componentintegral component of plasma membrane
C0031226cellular_componentintrinsic component of plasma membrane
C0016020cellular_componentmembrane
C0043025cellular_componentneuronal cell body
C0005886cellular_componentplasma membrane
C0045211cellular_componentpostsynaptic membrane
C0045202cellular_componentsynapse
C0005524molecular_functionATP binding
C0015278molecular_functioncalcium-release channel activity
C0005516molecular_functioncalmodulin binding
C0005261molecular_functioncation channel activity
C0008324molecular_functioncation transmembrane transporter activity
C0017081molecular_functionchloride channel regulator activity
C0005231molecular_functionexcitatory extracellular ligand-gated ion channel activity
C0005230molecular_functionextracellular ligand-gated ion channel activity
C0042802molecular_functionidentical protein binding
C0015276molecular_functionligand-gated ion channel activity
C0046872molecular_functionmetal ion binding
C0035091molecular_functionphosphatidylinositol binding
C0051219molecular_functionphosphoprotein binding
C0097603molecular_functiontemperature-gated ion channel activity
C0004888molecular_functiontransmembrane signaling receptor activity
C0048266biological_processbehavioral response to pain
C1990035
C0070588biological_processcalcium ion transmembrane transport
C0006816biological_processcalcium ion transport
C0071468biological_processcellular response to acidic pH
C0071312biological_processcellular response to alkaloid
C0071318biological_processcellular response to ATP
C0071345biological_processcellular response to cytokine stimulus
C0071363biological_processcellular response to growth factor stimulus
C0034605biological_processcellular response to heat
C1990090biological_processcellular response to nerve growth factor stimulus
C0071502biological_processcellular response to temperature stimulus
C0071356biological_processcellular response to tumor necrosis factor
C0050968biological_processdetection of chemical stimulus involved in sensory perception of pain
C0050965biological_processdetection of temperature stimulus involved in sensory perception of pain
C0050960biological_processdetection of temperature stimulus involved in thermoception
C0002024biological_processdiet induced thermogenesis
C0001660biological_processfever generation
C0014047biological_processglutamate secretion
C0006954biological_processinflammatory response
C0006629biological_processlipid metabolic process
C0001774biological_processmicroglial cell activation
C0090212biological_processnegative regulation of establishment of blood-brain barrier
C0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
C0002790biological_processpeptide secretion
C0043065biological_processpositive regulation of apoptotic process
C0007204biological_processpositive regulation of cytosolic calcium ion concentration
C0060454biological_processpositive regulation of gastric acid secretion
C0045429biological_processpositive regulation of nitric oxide biosynthetic process
C0051289biological_processprotein homotetramerization
C1901594biological_processresponse to capsazepine
C0009408biological_processresponse to heat
C0043434biological_processresponse to peptide hormone
C0009268biological_processresponse to pH
C0050954biological_processsensory perception of mechanical stimulus
C0060083biological_processsmooth muscle contraction involved in micturition
D0030054cellular_componentcell junction
D0005829cellular_componentcytosol
D0030425cellular_componentdendrite
D0032591cellular_componentdendritic spine membrane
D0009897cellular_componentexternal side of plasma membrane
D0016021cellular_componentintegral component of membrane
D0005887cellular_componentintegral component of plasma membrane
D0031226cellular_componentintrinsic component of plasma membrane
D0016020cellular_componentmembrane
D0043025cellular_componentneuronal cell body
D0005886cellular_componentplasma membrane
D0045211cellular_componentpostsynaptic membrane
D0045202cellular_componentsynapse
D0005524molecular_functionATP binding
D0015278molecular_functioncalcium-release channel activity
D0005516molecular_functioncalmodulin binding
D0005261molecular_functioncation channel activity
D0008324molecular_functioncation transmembrane transporter activity
D0017081molecular_functionchloride channel regulator activity
D0005231molecular_functionexcitatory extracellular ligand-gated ion channel activity
D0005230molecular_functionextracellular ligand-gated ion channel activity
D0042802molecular_functionidentical protein binding
D0015276molecular_functionligand-gated ion channel activity
D0046872molecular_functionmetal ion binding
D0035091molecular_functionphosphatidylinositol binding
D0051219molecular_functionphosphoprotein binding
D0097603molecular_functiontemperature-gated ion channel activity
D0004888molecular_functiontransmembrane signaling receptor activity
D0048266biological_processbehavioral response to pain
D1990035
D0070588biological_processcalcium ion transmembrane transport
D0006816biological_processcalcium ion transport
D0071468biological_processcellular response to acidic pH
D0071312biological_processcellular response to alkaloid
D0071318biological_processcellular response to ATP
D0071345biological_processcellular response to cytokine stimulus
D0071363biological_processcellular response to growth factor stimulus
D0034605biological_processcellular response to heat
D1990090biological_processcellular response to nerve growth factor stimulus
D0071502biological_processcellular response to temperature stimulus
D0071356biological_processcellular response to tumor necrosis factor
D0050968biological_processdetection of chemical stimulus involved in sensory perception of pain
D0050965biological_processdetection of temperature stimulus involved in sensory perception of pain
D0050960biological_processdetection of temperature stimulus involved in thermoception
D0002024biological_processdiet induced thermogenesis
D0001660biological_processfever generation
D0014047biological_processglutamate secretion
D0006954biological_processinflammatory response
D0006629biological_processlipid metabolic process
D0001774biological_processmicroglial cell activation
D0090212biological_processnegative regulation of establishment of blood-brain barrier
D0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
D0002790biological_processpeptide secretion
D0043065biological_processpositive regulation of apoptotic process
D0007204biological_processpositive regulation of cytosolic calcium ion concentration
D0060454biological_processpositive regulation of gastric acid secretion
D0045429biological_processpositive regulation of nitric oxide biosynthetic process
D0051289biological_processprotein homotetramerization
D1901594biological_processresponse to capsazepine
D0009408biological_processresponse to heat
D0043434biological_processresponse to peptide hormone
D0009268biological_processresponse to pH
D0050954biological_processsensory perception of mechanical stimulus
D0060083biological_processsmooth muscle contraction involved in micturition
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Functional Information from PDB Data

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

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> Sequence Neighbor

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