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- EMDB-39151: structure of human trpv1 in complex with BC5 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39151
Titlestructure of human trpv1 in complex with BC5
Map data
Sample
  • Complex: BC5
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (1~{R},2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)-1-[5-[(2~{S})-2-[(2,6-dimethylphenyl)carbamoyl]piperidin-1-yl]pentyl]piperidin-1-ium-2-carboxamide
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: SODIUM ION
KeywordsION CHANNEL / MEMBRANE PROTEIN / CRYO-EM
Function / homology
Function and homology information


chemosensory behavior / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition ...chemosensory behavior / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / fever generation / thermoception / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / dendritic spine membrane / chloride channel regulator activity / glutamate secretion / TRP channels / negative regulation of heart rate / cellular response to ATP / cellular response to alkaloid / diet induced thermogenesis / intracellularly gated calcium channel activity / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / voltage-gated calcium channel activity / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / GABA-ergic synapse / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / lipid metabolic process / calcium channel activity / calcium ion transmembrane transport / response to peptide hormone / transmembrane signaling receptor activity / positive regulation of nitric oxide biosynthetic process / sensory perception of taste / cellular response to tumor necrosis factor / cellular response to heat / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / postsynaptic membrane / cell surface receptor signaling pathway / calmodulin binding / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / negative regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / membrane / metal ion binding / 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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsKe BW / Hu SL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Sequential multitarget modulation: Developing Ultra-long-acting sensory-specific local anesthetics for postoperative pain
Authors: Hu SL / Wenrui G
History
DepositionFeb 18, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39151.png

Downloads & links

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Map

FileDownload / File: emd_39151.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 294.84 Å		0.82 Å/pix.
x 360 pix.
= 294.84 Å		0.82 Å/pix.
x 360 pix.
= 294.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.172
Minimum - Maximum-0.16274828 - 0.4017201
Average (Standard dev.)0.00029099238 (±0.012429559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 294.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : BC5

EntireName: BC5
Components
  • Complex: BC5
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (1~{R},2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)-1-[5-[(2~{S})-2-[(2,6-dimethylphenyl)carbamoyl]piperidin-1-yl]pentyl]piperidin-1-ium-2-carboxamide
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: SODIUM ION

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Supramolecule #1: BC5

SupramoleculeName: BC5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 1

MacromoleculeName: Transient receptor potential cation channel subfamily V member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.308023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLYDRRSIF EAVAQNNCQD LESLLLFLQK SKKHLTDNEF KDPETGKTCL LKAMLNLHDG QNTTIPLLLE IARQTDSLKE LVNASYTDS YYKGQTALHI AIERRNMALV TLLVENGADV QAAAHGDFFK KTKGRPGFYF GELPLSLAAC TNQLGIVKFL L QNSWQTAD ...String:
MRLYDRRSIF EAVAQNNCQD LESLLLFLQK SKKHLTDNEF KDPETGKTCL LKAMLNLHDG QNTTIPLLLE IARQTDSLKE LVNASYTDS YYKGQTALHI AIERRNMALV TLLVENGADV QAAAHGDFFK KTKGRPGFYF GELPLSLAAC TNQLGIVKFL L QNSWQTAD ISARDSVGNT VLHALVEVAD NTADNTKFVT SMYNEILMLG AKLHPTLKLE ELTNKKGMTP LALAAGTGKI GV LAYILQR EIQEPECRHL SRKFTEWAYG PVHSSLYDLS CIDTCEKNSV LEVIAYSSSE TPNRHDMLLV EPLNRLLQDK WDR FVKRIF YFNFLVYCLY MIIFTMAAYY RPVDGLPPFK MEKTGDYFRV TGEILSVLGG VYFFFRGIQY FLQRRPSMKT LFVD SYSEM LFFLQSLFML ATVVLYFSHL KEYVASMVFS LALGWTNMLY YTRGFQQMGI YAVMIEKMIL RDLCRFMFVY IVFLF GFST AVVTLIEDGK NDSLPSESTS HRWRGPACRP PDSSYNSLYS TCLELFKFTI GMGDLEFTEN YDFKAVFIIL LLAYVI LTY ILLLNMLIAL MGETVNKIAQ ESKNIWKLQR AITILDTEKS FLKCMRKAFR SGKLLQVGYT PDGKDDYRWC FRVDEVN WT TWNTNVGIIN EDPG

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: (1~{R},2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)-1-[5-[(2~{S})-2-[...

MacromoleculeName: (1~{R},2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)-1-[5-[(2~{S})-2-[(2,6-dimethylphenyl)carbamoyl]piperidin-1-yl]pentyl]piperidin-1-ium-2-carboxamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1LZ2
Molecular weightTheoretical: 589.874 Da

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Macromolecule #3: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 3 / Number of copies: 4 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8df9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 729166
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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