[English] 日本語
Yorodumi
- EMDB-65639: Structure of rat TRPV1 in complex with SB-366791 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65639
TitleStructure of rat TRPV1 in complex with SB-366791
Map data
Sample
  • Complex: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide
KeywordsTRPV1 / protein complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / cellular response to temperature stimulus / peptide secretion / smooth muscle contraction involved in micturition / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels ...negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / cellular response to temperature stimulus / peptide secretion / smooth muscle contraction involved in micturition / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels / fever generation / detection of temperature stimulus involved in thermoception / urinary bladder smooth muscle contraction / thermoception / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / response to pH / chloride channel regulator activity / dendritic spine membrane / monoatomic cation transmembrane transporter activity / glutamate secretion / ligand-gated monoatomic ion channel activity / negative regulation of heart rate / response to pain / temperature homeostasis / diet induced thermogenesis / cellular response to alkaloid / cellular response to ATP / 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 / calcium ion import across plasma membrane / monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to peptide hormone / calcium ion transmembrane transport / GABA-ergic synapse / lipid metabolic process / cellular response to growth factor stimulus / calcium channel activity / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / transmembrane signaling receptor activity / calcium ion transport / sensory perception of taste / 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 / 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: 3.25 Å
AuthorsChen X / Yu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371289 China
CitationJournal: To Be Published
Title: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
Authors: Yu Y
History
DepositionJul 31, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65639.png

Downloads & links

-
Map

FileDownload / File: emd_65639.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.107
Minimum - Maximum-0.54918504 - 0.8147074
Average (Standard dev.)0.0012552629 (±0.028171543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_65639_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65639_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of rat TRPV1 in complex with the analgesic drug...

EntireName: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
Components
  • Complex: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide

-
Supramolecule #1: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug...

SupramoleculeName: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
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: 99.514625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFKGLVD MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRL FGKGDSEEAS PLDCPYEEGG LASCPIITVS SVLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD A VAQSNCQE ...String:
DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFKGLVD MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRL FGKGDSEEAS PLDCPYEEGG LASCPIITVS SVLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD A VAQSNCQE LESLLPFLQR SKKRLTDSEF KDPETGKTCL LKAMLNLHNG QNDTIALLLD VARKTDSLKQ FVNASYTDSY YK GQTALHI AIERRNMTLV TLLVENGADV QAAANGDFFK KTKGRPGFYF GELPLSLAAC TNQLAIVKFL LQNSWQPADI SAR DSVGNT VLHALVEVAD NTVDNTKFVT SMYNEILILG AKLHPTLKLE EITNRKGLTP LALAASSGKI GVLAYILQRE IHEP ECRHL SRKFTEWAYG PVHSSLYDLS CIDTCEKNSV LEVIAYSSSE TPNRHDMLLV EPLNRLLQDK WDRFVKRIFY FNFFV YCLY MIIFTAAAYY RPVEGLPPYK LKNTVGDYFR VTGEILSVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQS LFM LVSVVLYFSQ RKEYVASMVF SLAMGWTNML YYTRGFQQMG IYAVMIEKMI LRDLCRFMFV YLVFLFGFST AVVTLIE DG KNNSLPMEST PHKCRGSACK PGNSYNSLYS TCLELFKFTI GMGDLEFTEN YDFKAVFIIL LLAYVILTYI LLLNMLIA L MGETVNKIAQ ESKNIWKLQR AITILDTEKS FLKCMRKAFR SGKLLQVGFT PDGKDDYRWC FRVDEVNWTT WNTNVGIIN EDPGNCEGVK RTLSFSLRSG RVSGRNWKNF ALVPLLRDAS TRDRHATQQE EVQLKHYTGS LKPEDAEVFK DSMVPGEK

UniProtKB: Transient receptor potential cation channel subfamily V member 1

-
Macromolecule #2: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide

MacromoleculeName: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: ZEI
Molecular weightTheoretical: 287.741 Da
Chemical component information

ChemComp-ZEI:
(2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8 / Details: 20 mM Hepes, 150 mM NaCl
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 15491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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