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- EMDB-23161: Cryo-EM structure of DkTx-bound minimal TRPV1 at the singly-bound... -

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Basic information

Entry
Database: EMDB / ID: EMD-23161
TitleCryo-EM structure of DkTx-bound minimal TRPV1 at the singly-bound state
Map data
Sample
  • Complex: minimal TRPV1 in nanodisc
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
Function / homology
Function and homology information


response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / cellular response to temperature stimulus / detection of chemical stimulus involved in sensory perception of pain / urinary bladder smooth muscle contraction / TRP channels ...response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / cellular response to temperature stimulus / detection of chemical stimulus involved in sensory perception of pain / 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 / glutamate secretion / monoatomic cation transmembrane transporter activity / negative regulation of heart rate / cellular response to ATP / ligand-gated monoatomic ion channel activity / 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 / 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 / calcium ion transmembrane transport / calcium channel activity / lipid metabolic process / response to peptide hormone / calcium ion transport / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / 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 / metal ion binding / identical protein binding / membrane / 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: 3.03 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 20, 2020-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing 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
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23161.png

Downloads & links

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Map

FileDownload / File: emd_23161.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8488 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.007
Minimum - Maximum-0.0355533 - 0.06339143
Average (Standard dev.)3.422633e-05 (±0.002046704)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0360.0630.000

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Supplemental data

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Half map: #1

Fileemd_23161_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_23161_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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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

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Supramolecule #1: minimal TRPV1 in nanodisc

SupramoleculeName: minimal TRPV1 in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: 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 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAMGSRLYDR RSIFDAVAQS NCQELESLLP FLQRSKKRLT DSEFKDPETG KTCLLKAMLN LHNGQNDTIA LLLDVARKTD SLKQFVNASY TDSYYKGQTA LHIAIERRNM TLVTLLVENG ADVQAAANGD FFKKTKGRPG FYFGELPLSL AACTNQLAIV KFLLQNSWQP ...String:
GAMGSRLYDR RSIFDAVAQS NCQELESLLP FLQRSKKRLT DSEFKDPETG KTCLLKAMLN LHNGQNDTIA LLLDVARKTD SLKQFVNASY TDSYYKGQTA LHIAIERRNM TLVTLLVENG ADVQAAANGD FFKKTKGRPG FYFGELPLSL AACTNQLAIV KFLLQNSWQP ADISARDSVG NTVLHALVEV ADNTVDNTKF VTSMYNEILI LGAKLHPTLK LEEITNRKGL TPLALAASSG KIGVLAYILQ REIHEPECRH LSRKFTEWAY GPVHSSLYDL SCIDTCEKNS VLEVIAYSSS ETPNRHDMLL VEPLNRLLQD KWDRFVKRIF YFNFFVYCLY MIIFTAAAYY RPVEGLPPYK LKNTVGDYFR VTGEILSVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQSLFML VSVVLYFSQR KEYVASMVFS LAMGWTNMLY YTRGFQQMGI YAVMIEKMIL RDLCRFMFVY LVFLFGFSTA VVTLIEDGKY NSLYSTCLEL FKFTIGMGDL EFTENYDFKA VFIILLLAYV ILTYILLLNM LIALMGETVN KIAQESKNIW KLQRAITILD TEKSFLKCMR KAFRSGKLLQ VGFTPDGKDD YRWCFRVDEV NWTTWNTNVG IINEDPG

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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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108641
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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