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- EMDB-7119: TRPV2 ion channel in partially closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-7119
TitleTRPV2 ion channel in partially closed state
Map dataTRPV2 ion channel in a partially closed state and with a deletion in the pore turret domain.
Sample
  • Complex: TRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 2
KeywordsTRP / channel / cation / closed / MEMBRANE PROTEIN
Function / homology
Function and homology information


growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / axonal growth cone / positive regulation of axon extension / monoatomic cation channel activity / endomembrane system / calcium channel activity ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / axonal growth cone / positive regulation of axon extension / monoatomic cation channel activity / endomembrane system / calcium channel activity / melanosome / lamellipodium / positive regulation of cold-induced thermogenesis / cell body / negative regulation of cell population proliferation / axon / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / 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 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDosey TL / Wang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008280 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structures of TRPV2 in distinct conformations provide insight into role of the pore turret.
Authors: Timothy L Dosey / Zhao Wang / Guizhen Fan / Zhixian Zhang / Irina I Serysheva / Wah Chiu / Theodore G Wensel /
Abstract: Cation channels of the transient receptor potential (TRP) family serve important physiological roles by opening in response to diverse intra- and extracellular stimuli that regulate their lower or ...Cation channels of the transient receptor potential (TRP) family serve important physiological roles by opening in response to diverse intra- and extracellular stimuli that regulate their lower or upper gates. Despite extensive studies, the mechanism coupling these gates has remained obscure. Previous structures have failed to resolve extracellular loops, known in the TRPV subfamily as 'pore turrets', which are proximal to the upper gates. We established the importance of the pore turret through activity assays and by solving structures of rat TRPV2, both with and without an intact turret at resolutions of 4.0 Å and 3.6 Å, respectively. These structures resolve the full-length pore turret and reveal fully open and partially open states of TRPV2, both with unoccupied vanilloid pockets. Our results suggest a mechanism by which physiological signals, such as lipid binding, can regulate the lower gate and couple to the upper gate through a pore-turret-facilitated mechanism.
History
DepositionNov 18, 2017-
Header (metadata) releaseJan 24, 2018-
Map releaseDec 5, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bo5
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7119_1.png

emd_7119_2.png

emd_7119_3.png

emd_7119_4.png

Downloads & links

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Map

FileDownload / File: emd_7119.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV2 ion channel in a partially closed state and with a deletion in the pore turret domain.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 220 pix.
= 270.6 Å		1.23 Å/pix.
x 220 pix.
= 270.6 Å		1.23 Å/pix.
x 220 pix.
= 270.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.025153792 - 0.06453739
Average (Standard dev.)0.00018316944 (±0.003981216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 270.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z270.600270.600270.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0250.0650.000

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Supplemental data

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Sample components

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Entire : TRPV2 in a partially open state and with a deletion in the pore t...

EntireName: TRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
Components
  • Complex: TRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 2

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Supramolecule #1: TRPV2 in a partially open state and with a deletion in the pore t...

SupramoleculeName: TRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 2

MacromoleculeName: Transient receptor potential cation channel subfamily V member 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 79.476828 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVSANGDLHL PISNEQCMPE NNGSLGFEAP TPDRFDRDRL FSVVSRGVPE ELTGLLEYLR WNSKYLTDSA YTEGSTGKTC LMKAVLNLQ DGVNACIMPL LQIDKDSGNP KPLVNAQCTD EFYQGHSALH IAIEKRSLQC VKLLVENGAD VHLRACGRFF Q KHQGTCFY ...String:
MVSANGDLHL PISNEQCMPE NNGSLGFEAP TPDRFDRDRL FSVVSRGVPE ELTGLLEYLR WNSKYLTDSA YTEGSTGKTC LMKAVLNLQ DGVNACIMPL LQIDKDSGNP KPLVNAQCTD EFYQGHSALH IAIEKRSLQC VKLLVENGAD VHLRACGRFF Q KHQGTCFY FGELPLSLAA CTKQWDVVTY LLENPHQPAS LEATDSLGNT VLHALVMIAD NSPENSALVI HMYDGLLQMG AR LCPTVQL EEISNHQGLT PLKLAAKEGK IEIFRHILQR EFSGPYQPLS RKFTEWCYGP VRVSLYDLSS VDSWEKNSVL EII AFHCKS PNRHRMVVLE PLNKLLQEKW DRLVSRFFFN FACYLVYMFI FTVVAYHQPS LDQPAIPSSK ATFGESMLLL GHIL ILLGG IYLLLGQLWY FWRRRLFIWI SFMDSYFEIL FLLQALLTVL SQVLRFMETE WYLPLLVLSL VLGWLNLLYY TRGFQ HTGI YSVMIQKVIL RDLLRFLLVY LVFLFGFAVA LVSLSREARS PKAPEDNNST VTEQPTVGQE EEPAPYRSIL DASLEL FKF TIGMGELAFQ EQLRFRGVVL LLLLAYVLLT YVLLLNMLIA LMSETVNHVA DNSWSIWKLQ KAISVLEMEN GYWWCRR KK HREGRLLKVG TRGDGTPDER WCFRVEEVNW AAWEKTLPTL SEDPTETSQV APA

UniProtKB: Transient receptor potential cation channel subfamily V member 2

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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

Concentration.5 mg/mL
BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 293 K

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 160100
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 50509
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)

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