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- EMDB-23136: cryo-EM structure of unliganded minimal TRPV1 -

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Basic information

Entry
Database: EMDB / ID: EMD-23136
Titlecryo-EM structure of unliganded minimal TRPV1
Map dataC4 symmetry imposed during data processing
Sample
  • Complex: minimal TRPV1 in nanodisc
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate
  • Ligand: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate
  • Ligand: SODIUM ION
KeywordsTRP channel / cryo-EM / nanodisc / TRANSPORT PROTEIN
Function / homology
Function and homology information


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 / urinary bladder smooth muscle contraction / TRP channels ...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 / urinary bladder smooth muscle contraction / TRP channels / 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 / response to pH / dendritic spine membrane / chloride channel regulator activity / monoatomic cation transmembrane transporter activity / glutamate secretion / negative regulation of heart rate / cellular response to ATP / response to pain / temperature homeostasis / cellular response to alkaloid / diet induced thermogenesis / cellular response to cytokine stimulus / 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 / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / GABA-ergic synapse / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / cellular response to growth factor stimulus / lipid metabolic process / calcium channel activity / calcium ion transmembrane transport / response to peptide hormone / calcium ion transport / 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 / response to heat / monoatomic ion transmembrane transport / protein homotetramerization / postsynaptic membrane / calmodulin binding / 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 / 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 speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang K / Julius D / Cheng Y
Funding support France, United States, 5 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000471/2017-L France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098672 United States
National Institutes of Health/Office of the DirectorS10 OD021741 United States
National Institutes of Health/Office of the DirectorS10 OD020054 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35 NS105038 United States
CitationJournal: Cell / Year: 2021
Title: Structural snapshots of TRPV1 reveal mechanism of polymodal functionality.
Authors: Kaihua Zhang / David Julius / Yifan Cheng /
Abstract: Many transient receptor potential (TRP) channels respond to diverse stimuli and conditionally conduct small and large cations. Such functional plasticity is presumably enabled by a uniquely dynamic ...Many transient receptor potential (TRP) channels respond to diverse stimuli and conditionally conduct small and large cations. Such functional plasticity is presumably enabled by a uniquely dynamic ion selectivity filter that is regulated by physiological agents. What is currently missing is a "photo series" of intermediate structural states that directly address this hypothesis and reveal specific mechanisms behind such dynamic channel regulation. Here, we exploit cryoelectron microscopy (cryo-EM) to visualize conformational transitions of the capsaicin receptor, TRPV1, as a model to understand how dynamic transitions of the selectivity filter in response to algogenic agents, including protons, vanilloid agonists, and peptide toxins, permit permeation by small and large organic cations. These structures also reveal mechanisms governing ligand binding substates, as well as allosteric coupling between key sites that are proximal to the selectivity filter and cytoplasmic gate. These insights suggest a general framework for understanding how TRP channels function as polymodal signal integrators.
History
DepositionDec 17, 2020-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l2p
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23136.png

Downloads & links

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Map

FileDownload / File: emd_23136.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC4 symmetry imposed during data processing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.015
Minimum - Maximum-0.09058757 - 0.21657746
Average (Standard dev.)0.000011475899 (±0.004849253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.104271.104271.104
α/β/γ90.00090.00090.000
start NX/NY/NZ10610885
NX/NY/NZ9087120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0910.2170.000

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Supplemental data

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Additional map: The map quality of Ankyrin repeats domain improved...

Fileemd_23136_additional_1.map
AnnotationThe map quality of Ankyrin repeats domain improved by symmetry expansion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_23136_half_map_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_23136_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : minimal TRPV1 in nanodisc

EntireName: minimal TRPV1 in nanodisc
Components
  • Complex: minimal TRPV1 in nanodisc
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate
  • Ligand: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate
  • Ligand: SODIUM ION

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Supramolecule #1: minimal TRPV1 in nanodisc

SupramoleculeName: minimal TRPV1 in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 73.016352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAMGSRLYDR RSIFDAVAQS NCQELESLLP FLQRSKKRLT DSEFKDPETG KTCLLKAMLN LHNGQNDTIA LLLDVARKTD SLKQFVNAS YTDSYYKGQT ALHIAIERRN MTLVTLLVEN GADVQAAANG DFFKKTKGRP GFYFGELPLS LAACTNQLAI V KFLLQNSW ...String:
GAMGSRLYDR RSIFDAVAQS NCQELESLLP FLQRSKKRLT DSEFKDPETG KTCLLKAMLN LHNGQNDTIA LLLDVARKTD SLKQFVNAS YTDSYYKGQT ALHIAIERRN MTLVTLLVEN GADVQAAANG DFFKKTKGRP GFYFGELPLS LAACTNQLAI V KFLLQNSW QPADISARDS VGNTVLHALV EVADNTVDNT KFVTSMYNEI LILGAKLHPT LKLEEITNRK GLTPLALAAS SG KIGVLAY ILQREIHEPE CRHLSRKFTE WAYGPVHSSL YDLSCIDTCE KNSVLEVIAY SSSETPNRHD MLLVEPLNRL LQD KWDRFV KRIFYFNFFV YCLYMIIFTA AAYYRPVEGL PPYKLKNTVG DYFRVTGEIL SVSGGVYFFF RGIQYFLQRR PSLK SLFVD SYSEILFFVQ SLFMLVSVVL YFSQRKEYVA SMVFSLAMGW TNMLYYTRGF QQMGIYAVMI EKMILRDLCR FMFVY LVFL FGFSTAVVTL IEDGKYNSLY STCLELFKFT IGMGDLEFTE NYDFKAVFII LLLAYVILTY ILLLNMLIAL MGETVN KIA QESKNIWKLQ RAITILDTEK SFLKCMRKAF RSGKLLQVGF TPDGKDDYRW CFRVDEVNWT TWNTNVGIIN EDPG

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5...

MacromoleculeName: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: XJ7
Molecular weightTheoretical: 600.633 Da
Chemical component information

ChemComp-XJ7:
(2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate

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Macromolecule #3: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~...

MacromoleculeName: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate
type: ligand / ID: 3 / Number of copies: 4 / Formula: 6IY
Molecular weightTheoretical: 565.72 Da
Chemical component information

ChemComp-6IY:
(10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate

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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: 7.4
Sugar embeddingMaterial: nanodisc
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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:

3j5p

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97601
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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