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- EMDB-7123: Cryo-EM structure of rat TRPV6* in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-7123
TitleCryo-EM structure of rat TRPV6* in nanodiscs
Map dataprimary map
Sample
  • Complex: TRPV6* ion channel in closed states
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 6
KeywordsIon channel / Membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion ...parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 6 / Transient receptor potential cation channel subfamily V member 5/6 / 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 6
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMcGoldrick LL / Singh AK / Saotome K / Yelshanskaya MV / Twomey EC / Grassucci RA / Sobolevsky AI
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA206573-01A1 United States
CitationJournal: Nature / Year: 2018
Title: Opening of the human epithelial calcium channel TRPV6.
Authors: Luke L McGoldrick / Appu K Singh / Kei Saotome / Maria V Yelshanskaya / Edward C Twomey / Robert A Grassucci / Alexander I Sobolevsky /
Abstract: Calcium-selective transient receptor potential vanilloid subfamily member 6 (TRPV6) channels play a critical role in calcium uptake in epithelial tissues. Altered TRPV6 expression is associated with ...Calcium-selective transient receptor potential vanilloid subfamily member 6 (TRPV6) channels play a critical role in calcium uptake in epithelial tissues. Altered TRPV6 expression is associated with a variety of human diseases, including cancers. TRPV6 channels are constitutively active and their open probability depends on the lipidic composition of the membrane in which they reside; it increases substantially in the presence of phosphatidylinositol 4,5-bisphosphate. Crystal structures of detergent-solubilized rat TRPV6 in the closed state have previously been solved. Corroborating electrophysiological results, these structures demonstrated that the Ca selectivity of TRPV6 arises from a ring of aspartate side chains in the selectivity filter that binds Ca tightly. However, how TRPV6 channels open and close their pores for ion permeation has remained unclear. Here we present cryo-electron microscopy structures of human TRPV6 in the open and closed states. The channel selectivity filter adopts similar conformations in both states, consistent with its explicit role in ion permeation. The iris-like channel opening is accompanied by an α-to-π-helical transition in the pore-lining transmembrane helix S6 at an alanine hinge just below the selectivity filter. As a result of this transition, the S6 helices bend and rotate, exposing different residues to the ion channel pore in the open and closed states. This gating mechanism, which defines the constitutive activity of TRPV6, is, to our knowledge, unique among tetrameric ion channels and provides structural insights for understanding their diverse roles in physiology and disease.
History
DepositionNov 18, 2017-
Header (metadata) releaseDec 6, 2017-
Map releaseDec 20, 2017-
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: 0.0432
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0432
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bob
  • Surface level: 0.0432
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7123.png

Downloads & links

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Map

FileDownload / File: emd_7123.map.gz / Format: CCP4 / Size: 32.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.0432 / Movie #1: 0.0432
Minimum - Maximum-0.14001907 - 0.18755873
Average (Standard dev.)0.0010047143 (±0.008897378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions204204204
Spacing204204204
CellA=B=C: 199.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z204204204
origin x/y/z0.0000.0000.000
length x/y/z199.920199.920199.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS204204204
D min/max/mean-0.1400.1880.001

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Supplemental data

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Sample components

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Entire : TRPV6* ion channel in closed states

EntireName: TRPV6* ion channel in closed states
Components
  • Complex: TRPV6* ion channel in closed states
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 6

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Supramolecule #1: TRPV6* ion channel in closed states

SupramoleculeName: TRPV6* ion channel in closed states / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 6

MacromoleculeName: Transient receptor potential cation channel subfamily V member 6
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 77.133492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSLPKEKG LILCLWNKFC RWFHRRESWA QSRDEQNLLQ QKRIWESPLL LAAKENNVQA LYKLLKFEGC EVHQKGAMGE TALHIAALY DNNEAAQVLM EAAPELVFEP MTSELYEGQT ALHIAVINQN VNLVRALLAR GASVSARATG SVFHYRPHNL I YYGEHPLS ...String:
MGWSLPKEKG LILCLWNKFC RWFHRRESWA QSRDEQNLLQ QKRIWESPLL LAAKENNVQA LYKLLKFEGC EVHQKGAMGE TALHIAALY DNNEAAQVLM EAAPELVFEP MTSELYEGQT ALHIAVINQN VNLVRALLAR GASVSARATG SVFHYRPHNL I YYGEHPLS FAACVGSEEI VRLLIEHGAD IRAQDSLGNT VLHILILQPN KTFACQMYNL LLSYDGGDHL KSLELVPNNQ GL TPFKLAG VEGNIVMFQH LMQKRKHIQW TYGPLTSTLY DLTEIDSSGD DQSLLELIVT TKKREARQIL DQTPVKELVS LKW KRYGRP YFCVLGAIYV LYIICFTMCC VYRPLKPRIT NRTNPRDNTL LQQKLLQEAY VTPKDDLRLV GELVSIVGAV IILL VEIPD IFRLGVTRFF GQTILGGPFH VIIVTYAFMV LVTMVMRLTN SDGEVVPMSF ALVLGWCNVM YFARGFQMLG PFTIM IQKM IFGDLMRFCW LMAVVILGFA SAFYIIFQTE DPDELGHFYD YPMALFSTFE LFLTIIDGPA NYDVDLPFMY SITYAA FAI IATLLMLNLL IAMMGDTHWR VAHERDELWR AQVVATTVML ERKLPRCLWP RSGICGREYG LGDRWFLRVE DRQDLNR QR IRRYAQAFQQ QDDLYSEDLE KDSGEKLVPR

UniProtKB: Transient receptor potential cation channel subfamily V member 6

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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

Concentration0.5 mg/mL
BufferpH: 8 / Component: (Formula: TRIS, NaClSodium chloride) / Details: TRIS, NaCl,
GridModel: C-flat-1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 248836
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5iwk

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 20808

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6bob:
Cryo-EM structure of rat TRPV6* in nanodiscs

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