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- EMDB-23138: Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state -

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Basic information

Entry
Database: EMDB / ID: EMD-23138
TitleCryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state
Map data
Sample
  • Complex: minimal TRPV1 in nanodisc
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
    • Protein or peptide: Tau-theraphotoxin-Hs1a
  • 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: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsTRP channel / cryo-EM / nanodisc / toxin / TRANSPORT PROTEIN
Function / homology
Function and homology information


temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus ...temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus / cellular response to acidic pH / fever generation / thermoception / detection of temperature stimulus involved in thermoception / ion channel regulator activity / negative regulation of systemic arterial blood pressure / glutamate secretion / response to pH / chloride channel regulator activity / dendritic spine membrane / monoatomic cation transmembrane transporter activity / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of heart rate / cellular response to ATP / temperature homeostasis / response to pain / cellular response to alkaloid / calcium ion import across plasma membrane / diet induced thermogenesis / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / intracellularly gated calcium channel activity / behavioral response to pain / negative regulation of mitochondrial membrane potential / ligand-gated monoatomic ion channel activity / extracellular ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / GABA-ergic synapse / sensory perception of pain / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / phosphoprotein binding / calcium ion transmembrane transport / microglial cell activation / calcium channel activity / lipid metabolic process / cellular response to growth factor stimulus / response to peptide hormone / calcium ion transport / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / cellular response to heat / positive regulation of cytosolic calcium ion concentration / toxin activity / response to heat / monoatomic ion transmembrane transport / postsynaptic membrane / protein homotetramerization / calmodulin binding / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / lipid binding / dendrite / negative regulation of transcription by RNA polymerase II / extracellular region / 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 / Tau-theraphotoxin-Hs1a
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Cyriopagopus schmidti (Chinese earth tiger)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l2r
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23138.png

Downloads & links

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Map

FileDownload / File: emd_23138.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.616 Å		0.85 Å/pix.
x 320 pix.
= 271.616 Å		0.85 Å/pix.
x 320 pix.
= 271.616 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8488 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045 / Movie #1: 0.007
Minimum - Maximum-0.031585574 - 0.052931387
Average (Standard dev.)0.000078951765 (±0.0018581445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.84880.84880.8488
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z271.616271.616271.616
α/β/γ90.00090.00090.000
start NX/NY/NZ10610885
NX/NY/NZ9087120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0320.0530.000

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Supplemental data

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Half map: #2

Fileemd_23138_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_23138_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 : 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
    • Protein or peptide: Tau-theraphotoxin-Hs1a
  • 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: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: minimal TRPV1 in nanodisc

SupramoleculeName: minimal TRPV1 in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: Tau-theraphotoxin-Hs1a

MacromoleculeName: Tau-theraphotoxin-Hs1a / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cyriopagopus schmidti (Chinese earth tiger)
Molecular weightTheoretical: 8.684185 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MDCAKEGEVC SWGKKCCDLD NFYCPMEFIP HCKKYKPYVP VTTNCAKEGE VCGWGSKCCH GLDCPLAFIP YCEKYR

UniProtKB: Tau-theraphotoxin-Hs1a

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Macromolecule #3: (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: 3 / 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 #4: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5...

MacromoleculeName: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate
type: ligand / ID: 4 / Number of copies: 4 / Formula: 65I
Molecular weightTheoretical: 481.56 Da
Chemical component information

ChemComp-65I:
(9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 K3 (6k x 4k) / Average electron dose: 67.0 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39680
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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