[English] 日本語
Yorodumi
- EMDB-23742: Zebrafish TRPM5 with 1 mM EDTA in nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23742
TitleZebrafish TRPM5 with 1 mM EDTA in nanodisc
Map dataNon-sharpened map for zebrafish TRPM5 with 1 mM EDTA in nanodisc
Sample
  • Complex: TRPM5 channel
    • Protein or peptide: zebrafish TRPM5
Function / homology
Function and homology information


ligand-gated calcium channel activity / calcium-activated cation channel activity / calcium ion transmembrane transport / calcium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical / TRPM, SLOG domain / : / SLOG in TRPM / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRuan Z / Lu W / Du J / Haley E
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R56HL144929 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS111031 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL153219 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS112363 United States
American Heart Association20POST35120556 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structures of the TRPM5 channel elucidate mechanisms of activation and inhibition.
Authors: Zheng Ruan / Emery Haley / Ian J Orozco / Mark Sabat / Richard Myers / Rebecca Roth / Juan Du / Wei Lü /
Abstract: The Ca-activated TRPM5 channel plays essential roles in taste perception and insulin secretion. However, the mechanism by which Ca regulates TRPM5 activity remains elusive. We report cryo-EM ...The Ca-activated TRPM5 channel plays essential roles in taste perception and insulin secretion. However, the mechanism by which Ca regulates TRPM5 activity remains elusive. We report cryo-EM structures of the zebrafish TRPM5 in an apo closed state, a Ca-bound open state, and an antagonist-bound inhibited state. We define two novel ligand binding sites: a Ca site (Ca) in the intracellular domain and an antagonist site in the transmembrane domain (TMD). The Ca site is unique to TRPM5 and has two roles: modulating the voltage dependence and promoting Ca binding to the Ca site, which is conserved throughout TRPM channels. Conformational changes initialized from both Ca sites cooperatively open the ion-conducting pore. The antagonist NDNA wedges into the space between the S1-S4 domain and pore domain, stabilizing the transmembrane domain in an apo-like closed state. Our results lay the foundation for understanding the voltage-dependent TRPM channels and developing new therapeutic agents.
History
DepositionApr 1, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23742.png

Downloads & links

-
Map

FileDownload / File: emd_23742.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharpened map for zebrafish TRPM5 with 1 mM EDTA in nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312.6 Å		1.04 Å/pix.
x 300 pix.
= 312.6 Å		1.04 Å/pix.
x 300 pix.
= 312.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.042 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.015
Minimum - Maximum-0.023028148 - 0.05981365
Average (Standard dev.)3.18869e-05 (±0.0027176475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0421.0421.042
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.600312.600312.600
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0230.0600.000

-
Supplemental data

-
Additional map: Sharpened map for zebrafish TRPM5 with 1 mM EDTA in nanodisc

Fileemd_23742_additional_1.map
AnnotationSharpened map for zebrafish TRPM5 with 1 mM EDTA in nanodisc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TRPM5 channel

EntireName: TRPM5 channel
Components
  • Complex: TRPM5 channel
    • Protein or peptide: zebrafish TRPM5

-
Supramolecule #1: TRPM5 channel

SupramoleculeName: TRPM5 channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Danio rerio (zebrafish)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: zebrafish TRPM5

MacromoleculeName: zebrafish TRPM5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
SequenceString: MVEKSSERFD KQMAGRLGDI DFTGVSRTRG KFVRVTSSTD PAEIYQILTK QWGLAPPHLV VALMGGDEV AQLKPWLRDT LRKGLVKAAQ STGAWILTSG LRFGITKNLG QAVRDHSLAS T SPKVRVVA IGIAPWNMIQ NRDLLLSAKP DHPATYPTED LPYGAVYSLD ...String:
MVEKSSERFD KQMAGRLGDI DFTGVSRTRG KFVRVTSSTD PAEIYQILTK QWGLAPPHLV VALMGGDEV AQLKPWLRDT LRKGLVKAAQ STGAWILTSG LRFGITKNLG QAVRDHSLAS T SPKVRVVA IGIAPWNMIQ NRDLLLSAKP DHPATYPTED LPYGAVYSLD CNHSHFILVD ED PKRPGAT GEMRVKMLKH ISLQRTGYGG TGSIEIPVLC LLVHGEPRIL QKMYKNIQNS IPW LILAGS GGVADILVTL MDRGCWDADI VQELLINTFP DGLHSTEITS WTKLIQRILD HGHL LTVHD PEQDSELDTV ILKALVKACK SQSQEAQDFL DELKLAVAWN RVDIAKSEIF SGDVQ WSAQ DLEEVMMEAL VNDKPDFVRL FVDNGVNIKQ FLTYGRLQEL YCSVSEKNLL HTLLLK KNQ ERQAQLARKR MSGNPNNELG DRKFRFTFHE VSKVLKDFLD DTCKGFYQKL PAERMGK GR LFHSQKNLPD MDRRCEHPWR DLFLWAILQN RQEMANYFWA MGPEAVAAAL VGCKIMKE M AHLATEAESA RSMKNAKYEQ FAMDLFSECY SNSEDRAYSL LVRKTCCWSK ATVLNIATL AEAKCFFAHD GVQALLTKVW WGAMRTDTSI SRLVLTFFIP PLVWTSLIKF NPEEQVSKDE GEPFAELDS LETEQALLLT DGDPVAGEGS AETAARSCSA TFIRVVLRRW NRFWSAPVTV F MGNVIMYF AFLILFSYVL LLDFRPPPPY GPSAAEIILY FWVFTLVLEE IRQSFFTDED MS ILKKMKL YVEDNWNKCD MVAISLFVVG LSCRMAMSTY EAGRTVLALD FMVFTLRLIH IFA IHKQLG PKIIIVERMI KDVFFFLFFL SVWLIAYGVT TQALLHPNDP RIDWVFRRAL YRPY LHIFG QIPLEEIDAA KMPDDNCTTD VQEIILGTLP PCPNIYANWL VILLLVIYLL VTNVL LLNL LIAMFSYTFQ VVQENADIFW KFQRYNLIVE YHSRPALAPP FIIISHITQA LLSFIK KTE NTQDLLEREL PSGLDQKLMT WETVQKENYL AKLEHEHRES SGERLRYTSS KVQTLLR MV GGFKDQEKRM ATVETEVRYC GEVLSWIAEC FHKSTLKCDR DAPKAPRSIA GSSRDQQP Q GAKRQQPGGH PAYGTDKKLP FIDH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 49.6 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

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Number images used: 13000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

+
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