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- EMDB-23129: Cryo-EM structure of full-length TRPV1 at pH6a state -

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Basic information

Entry
Database: EMDB / ID: EMD-23129
TitleCryo-EM structure of full-length TRPV1 at pH6a state
Map data
Sample
  • Complex: full-length TRPV1 in nanodisc at pH6a state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate
KeywordsTRP channel / cryo-EM / nanodisc / full length / proton / 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 / response to pH / negative regulation of systemic arterial blood pressure / 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 / response to heat / positive regulation of cytosolic calcium ion concentration / 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: 3.7 Å
AuthorsZhang K / Julius D
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-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l2i
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23129.png

Downloads & links

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Map

FileDownload / File: emd_23129.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 224 pix.
= 257.6 Å		1.15 Å/pix.
x 224 pix.
= 257.6 Å		1.15 Å/pix.
x 224 pix.
= 257.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.014
Minimum - Maximum-0.07292601 - 0.110689685
Average (Standard dev.)0.000031474043 (±0.003763901)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 257.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z257.600257.600257.600
α/β/γ90.00090.00090.000
start NX/NY/NZ10610885
NX/NY/NZ9087120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0730.1110.000

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Supplemental data

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Half map: #1

Fileemd_23129_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_23129_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : full-length TRPV1 in nanodisc at pH6a state

EntireName: full-length TRPV1 in nanodisc at pH6a state
Components
  • Complex: full-length TRPV1 in nanodisc at pH6a state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate

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Supramolecule #1: full-length TRPV1 in nanodisc at pH6a state

SupramoleculeName: full-length TRPV1 in nanodisc at pH6a state / 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: 95.328156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAMGSEQRAS LDSEESESPP QENSCLDPPD RDPNCKPPPV KPHIFTTRSR TRLFGKGDSE EASPLDCPYE EGGLASCPII TVSSVLTIQ RPGDGPASVR PSSQDSVSAG EKPPRLYDRR SIFDAVAQSN CQELESLLPF LQRSKKRLTD SEFKDPETGK T CLLKAMLN ...String:
GAMGSEQRAS LDSEESESPP QENSCLDPPD RDPNCKPPPV KPHIFTTRSR TRLFGKGDSE EASPLDCPYE EGGLASCPII TVSSVLTIQ RPGDGPASVR PSSQDSVSAG EKPPRLYDRR SIFDAVAQSN CQELESLLPF LQRSKKRLTD SEFKDPETGK T CLLKAMLN LHNGQNDTIA LLLDVARKTD SLKQFVNASY TDSYYKGQTA LHIAIERRNM TLVTLLVENG ADVQAAANGD FF KKTKGRP GFYFGELPLS LAACTNQLAI VKFLLQNSWQ PADISARDSV GNTVLHALVE VADNTVDNTK FVTSMYNEIL ILG AKLHPT LKLEEITNRK GLTPLALAAS SGKIGVLAYI LQREIHEPEC RHLSRKFTEW AYGPVHSSLY DLSCIDTCEK NSVL EVIAY SSSETPNRHD MLLVEPLNRL LQDKWDRFVK RIFYFNFFVY CLYMIIFTAA AYYRPVEGLP PYKLKNTVGD YFRVT GEIL SVSGGVYFFF RGIQYFLQRR PSLKSLFVDS YSEILFFVQS LFMLVSVVLY FSQRKEYVAS MVFSLAMGWT NMLYYT RGF QQMGIYAVMI EKMILRDLCR FMFVYLVFLF GFSTAVVTLI EDGKNNSLPM ESTPHKCRGS ACKPGNSYNS LYSTCLE LF KFTIGMGDLE FTENYDFKAV FIILLLAYVI LTYILLLNML IALMGETVNK IAQESKNIWK LQRAITILDT EKSFLKCM R KAFRSGKLLQ VGFTPDGKDD YRWCFRVDEV NWTTWNTNVG IINEDPGNCE GVKRTLSFSL RSGRVSGRNW KNFALVPLL RDASTRDRHA TQQEEVQLKH YTGSLKPEDA EVFKDSMVPG EK

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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

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

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

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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: 6
Sugar embeddingMaterial: nanodisc
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 76.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41166
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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