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- PDB-9ogk: Refinement of PDB-3J5R against EMD-8117 using EMAN2 -

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Basic information

Entry
Database: PDB / ID: 9ogk
TitleRefinement of PDB-3J5R against EMD-8117 using EMAN2
ComponentsTransient receptor potential cation channel subfamily V member 1
KeywordsMEMBRANE PROTEIN / TRPV1
Function / homology
Function and homology information


peptide secretion / negative regulation of iodide transmembrane transport / detection of temperature stimulus involved in thermoception / sensory perception of mechanical stimulus / negative regulation of establishment of blood-brain barrier / positive regulation of renal sodium excretion / response to capsazepine / cellular response to temperature stimulus / detection of chemical stimulus involved in sensory perception of pain / positive regulation of sensory perception of pain ...peptide secretion / negative regulation of iodide transmembrane transport / detection of temperature stimulus involved in thermoception / sensory perception of mechanical stimulus / negative regulation of establishment of blood-brain barrier / positive regulation of renal sodium excretion / response to capsazepine / cellular response to temperature stimulus / detection of chemical stimulus involved in sensory perception of pain / positive regulation of sensory perception of pain / temperature-gated ion channel activity / smooth muscle contraction involved in micturition / fever generation / negative regulation of axon regeneration / diet induced thermogenesis / positive regulation of membrane depolarization / TRP channels / positive regulation of cardiac muscle cell differentiation / urinary bladder smooth muscle contraction / thermoception / glutamate secretion / response to pH / cellular response to alkaloid / monoatomic cation transmembrane transporter activity / response to pain / response to acidic pH / negative regulation of systemic arterial blood pressure / dendritic spine membrane / excitatory extracellular ligand-gated monoatomic ion channel activity / positive regulation of urine volume / negative regulation of heart rate / temperature homeostasis / sensory perception of taste / behavioral response to pain / cellular response to cytokine stimulus / cellular response to ATP / intracellularly gated calcium channel activity / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / positive regulation of vasoconstriction / monoatomic ion channel activity / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / cellular response to acidic pH / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / axon terminus / positive regulation of excitatory postsynaptic potential / lipid metabolic process / cellular response to tumor necrosis factor / sarcoplasmic reticulum / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / cellular response to growth factor stimulus / response to peptide hormone / GABA-ergic synapse / positive regulation of nitric oxide biosynthetic process / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / positive regulation of cytosolic calcium ion concentration / response to heat / monoatomic ion transmembrane transport / protein homotetramerization / calmodulin binding / postsynaptic membrane / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / 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 / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsChen, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150905 United States
Citation
Journal: Nature / Year: 2016
Title: TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.
Authors: Yuan Gao / Erhu Cao / David Julius / Yifan Cheng /
Abstract: When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. ...When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. This is especially relevant to proteins for which lipids have both structural and regulatory roles. Here we demonstrate the power of combining electron cryo-microscopy with lipid nanodisc technology to ascertain the structure of the rat TRPV1 ion channel in a native bilayer environment. Using this approach, we determined the locations of annular and regulatory lipids and showed that specific phospholipid interactions enhance binding of a spider toxin to TRPV1 through formation of a tripartite complex. Furthermore, phosphatidylinositol lipids occupy the binding site for capsaicin and other vanilloid ligands, suggesting a mechanism whereby chemical or thermal stimuli elicit channel activation by promoting the release of bioactive lipids from a critical allosteric regulatory site.
#1: Journal: bioRxiv / Year: 2024
Title: Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks.
Authors: Muyuan Chen /
Abstract: Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can ...Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores.
History
DepositionApr 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Remark 0THIS ENTRY 9OGK CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP EMD-8117 DETERMINED ...THIS ENTRY 9OGK CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP EMD-8117 DETERMINED ORIGINALLY BY AUTHORS: Gao, Y., Cao, E., Julius, D., Cheng, Y.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transient receptor potential cation channel subfamily V member 1
A: Transient receptor potential cation channel subfamily V member 1
C: Transient receptor potential cation channel subfamily V member 1
D: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)380,2244
Polymers380,2244
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 1 / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid ...TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid receptor type 1-like


Mass: 95055.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv1, Vr1, Vr1l / Production host: Homo sapiens (human) / References: UniProt: O35433
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: Reconstruction of TRPV1 ion channel in complex with capsaicin by single particle cryo-microscopy
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 21 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7EMAN22.99.66model fitting
13EMAN22.99.66model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33238 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3J5R

3j5r


Accession code: 3J5R / Details: refine starting from pdb / Source name: PDB / Type: experimental model

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