[English] 日本語
Yorodumi
- EMDB-40940: TRPV1 in Nanodisc bound with lysophosphatidic acid in all four mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40940
TitleTRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers
Map dataTRPV1 in nanodisc bound with LPA in all four monomers.
Sample
  • Complex: TRPV1 in nanodisc bound with lysophosphatidic acid in all four monomers
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1TRPV1
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate
  • Ligand: SODIUM IONSodium
KeywordsTRPV1 / lysophosphatidic acid / MEMBRANE PROTEIN
Function / homology
Function and homology information


temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 / cellular response to temperature stimulus / smooth muscle contraction involved in micturition ...temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / TRP channels / cellular response to acidic pH / thermoception / fever generation / detection of temperature stimulus involved in thermoception / glutamate secretion / dendritic spine membrane / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / response to pain / temperature homeostasis / negative regulation of heart rate / cellular response to alkaloid / behavioral response to pain / diet induced thermogenesis / extracellular ligand-gated monoatomic ion channel activity / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / sensory perception of pain / response to organonitrogen compound / phosphatidylinositol binding / monoatomic ion transmembrane transport / cellular response to nerve growth factor stimulus / phosphoprotein binding / calcium ion transmembrane transport / microglial cell activation / calcium channel activity / lipid metabolic process / response to peptide hormone / cellular response to growth factor stimulus / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / response to heat / postsynaptic membrane / protein homotetramerization / 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 / membrane / identical protein binding / 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: 3.5 Å
AuthorsArnold WR / Cheng Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of TRPV1 modulation by endogenous bioactive lipids.
Authors: William R Arnold / Adamo Mancino / Frank R Moss / Adam Frost / David Julius / Yifan Cheng /
Abstract: TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for ...TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli.
History
DepositionMay 31, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40940.png

Downloads & links

-
Map

FileDownload / File: emd_40940.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV1 in nanodisc bound with LPA in all four monomers.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 384 pix.
= 320.64 Å		0.84 Å/pix.
x 384 pix.
= 320.64 Å		0.84 Å/pix.
x 384 pix.
= 320.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-29.924689999999998 - 34.968006000000003
Average (Standard dev.)-0.000000000000407 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 320.63998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A for TRPV1 in nanodisc bound with LPA in all four monomers.

Fileemd_40940_half_map_1.map
AnnotationHalf Map A for TRPV1 in nanodisc bound with LPA in all four monomers.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B for TRPV1 in nanodisc bound with LPA in all four monomers.

Fileemd_40940_half_map_2.map
AnnotationHalf Map B for TRPV1 in nanodisc bound with LPA in all four monomers.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TRPV1 in nanodisc bound with lysophosphatidic acid in all four mo...

EntireName: TRPV1 in nanodisc bound with lysophosphatidic acid in all four monomers
Components
  • Complex: TRPV1 in nanodisc bound with lysophosphatidic acid in all four monomers
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1TRPV1
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate
  • Ligand: SODIUM IONSodium

-
Supramolecule #1: TRPV1 in nanodisc bound with lysophosphatidic acid in all four mo...

SupramoleculeName: TRPV1 in nanodisc bound with lysophosphatidic acid in all four monomers
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 688 KDa

-
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: 92.654172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG ...String:
MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG QNDTIALLLD VARKTDSLKQ FVNASYTDSY YKGQTALHIA IERRNMTLVT LLVENGADVQ AAANGDFFKK TK GRPGFYF GELPLSLAAC TNQLAIVKFL LQNSWQPADI SARDSVGNTV LHALVEVADN TVDNTKFVTS MYNEILILGA KLH PTLKLE EITNRKGLTP LALAASSGKI GVLAYILQRE IHEPECRHLS RKFTEWAYGP VHSSLYDLSC IDTCEKNSVL EVIA YSSSE TPNRHDMLLV EPLNRLLQDK WDRFVKRIFY FNFFVYCLYM IIFTAAAYYR PVEGLPPYKL KNTVGDYFRV TGEIL SVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQSLFML VSVVLYFSQR KEYVASMVFS LAMGWTNMLY YTRGFQ QMG IYAVMIEKMI LRDLCRFMFV YLVFLFGFST AVVTLIEDGK YNSLYSTCLE LFKFTIGMGD LEFTENYDFK AVFIILL LA YVILTYILLL NMLIALMGET VNKIAQESKN IWKLQRAITI LDTEKSFLKC MRKAFRSGKL LQVGFTPDGK DDYRWCFR V DEVNWTTWNT NVGIINEDPG NCEGVKRTLS FSLRSGRVSG RNWKNFALVP LLRDASTRDR HATQQEEVQL KHYTGSLKP EDAEVFKDSM VPGEK

UniProtKB: Transient receptor potential cation channel subfamily V member 1

-
Macromolecule #2: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate

MacromoleculeName: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate / type: ligand / ID: 2 / Number of copies: 4 / Formula: NKN
Molecular weightTheoretical: 382.429 Da
Chemical component information

ChemComp-NKN:
(2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate

-
Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8118

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11119
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more