[English] 日本語
Yorodumi
- EMDB-23740: Cryo-EM structure of zebrafish TRPM5 in the presence of 1 mM EDTA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23740
TitleCryo-EM structure of zebrafish TRPM5 in the presence of 1 mM EDTA
Map dataNon-sharpened map of zebrafish TRPM5 with 1 mM EDTA
Sample
  • Complex: TRPM5 channel
    • Protein or peptide: Transient receptor potential melastatin 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (25R)-14beta,17beta-spirost-5-en-3beta-ol
  • Ligand: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
Function / homology
Function and homology information


ligand-gated calcium channel activity / calcium-activated cation channel activity / calcium ion transmembrane transport / 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 melastatin 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateSep 22, 2021-
Current statusSep 22, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0183
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0183
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7mbp
  • Surface level: 0.0183
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23740.png

Downloads & links

-
Map

FileDownload / File: emd_23740.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharpened map of zebrafish TRPM5 with 1 mM EDTA
Voxel sizeX=Y=Z: 1.042 Å
Density
Contour LevelBy AUTHOR: 0.0183 / Movie #1: 0.0183
Minimum - Maximum-0.022561792 - 0.08109263
Average (Standard dev.)8.024221e-05 (±0.003724464)
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/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0230.0810.000

-
Supplemental data

-
Additional map: Sharpened map of zebrafish TRPM5 with 1 mM EDTA

Fileemd_23740_additional_1.map
AnnotationSharpened map of zebrafish TRPM5 with 1 mM EDTA
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: Transient receptor potential melastatin 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (25R)-14beta,17beta-spirost-5-en-3beta-ol
  • Ligand: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

-
Supramolecule #1: TRPM5 channel

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

-
Macromolecule #1: Transient receptor potential melastatin 5

MacromoleculeName: Transient receptor potential melastatin 5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 132.799 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVEKSSERFD KQMAGRLGDI DFTGVSRTRG KFVRVTSSTD PAEIYQILTK QWGLAPPHLV VALMGGDEVA QLKPWLRDTL RKGLVKAAQ STGAWILTSG LRFGITKNLG QAVRDHSLAS TSPKVRVVAI GIAPWNMIQN RDLLLSAKPD HPATYPTEDL P YGAVYSLD ...String:
MVEKSSERFD KQMAGRLGDI DFTGVSRTRG KFVRVTSSTD PAEIYQILTK QWGLAPPHLV VALMGGDEVA QLKPWLRDTL RKGLVKAAQ STGAWILTSG LRFGITKNLG QAVRDHSLAS TSPKVRVVAI GIAPWNMIQN RDLLLSAKPD HPATYPTEDL P YGAVYSLD CNHSHFILVD EDPKRPGATG EMRVKMLKHI SLQRTGYGGT GSIEIPVLCL LVHGEPRILQ KMYKNIQNSI PW LILAGSG GVADILVTLM DRGCWDADIV QELLINTFPD GLHSTEITSW TKLIQRILDH GHLLTVHDPE QDSELDTVIL KAL VKACKS QSQEAQDFLD ELKLAVAWNR VDIAKSEIFS GDVQWSAQDL EEVMMEALVN DKPDFVRLFV DNGVNIKQFL TYGR LQELY CSVSEKNLLH TLLLKKNQER QAQLARKRMS GNPNNELGDR KFRFTFHEVS KVLKDFLDDT CKGFYQKLPA ERMGK GRLF HSQKNLPDMD RRCEHPWRDL FLWAILQNRQ EMANYFWAMG PEAVAAALVG CKIMKEMAHL ATEAESARSM KNAKYE QFA MDLFSECYSN SEDRAYSLLV RKTCCWSKAT VLNIATLAEA KCFFAHDGVQ ALLTKVWWGA MRTDTSISRL VLTFFIP PL VWTSLIKFNP EEQVSKDEGE PFAELDSLET EQALLLTDGD PVAGEGSAET AARSCSATFI RVVLRRWNRF WSAPVTVF M GNVIMYFAFL ILFSYVLLLD FRPPPPYGPS AAEIILYFWV FTLVLEEIRQ SFFTDEDMSI LKKMKLYVED NWNKCDMVA ISLFVVGLSC RMAMSTYEAG RTVLALDFMV FTLRLIHIFA IHKQLGPKII IVERMIKDVF FFLFFLSVWL IAYGVTTQAL LHPNDPRID WVFRRALYRP YLHIFGQIPL EEIDAAKMPD DNCTTDVQEI ILGTLPPCPN IYANWLVILL LVIYLLVTNV L LLNLLIAM FSYTFQVVQE NADIFWKFQR YNLIVEYHSR PALAPPFIII SHITQALLSF IKKTENTQDL LERELPSGLD QK LMTWETV QKENYLAKLE HEHRESSGER LRYTSSKVQT LLRMVGGFKD QEKRMATVET EVRYCGEVLS WIAECFHKST LKC DRDAPK APRSIAGSSR DQQPQGAKRQ QPGGHPAYGT DKKLPFIDH

-
Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #3: (25R)-14beta,17beta-spirost-5-en-3beta-ol

MacromoleculeName: (25R)-14beta,17beta-spirost-5-en-3beta-ol / type: ligand / ID: 3 / Number of copies: 4 / Formula: YUV
Molecular weightTheoretical: 414.621 Da
Chemical component information

ChemComp-YUV:
(25R)-14beta,17beta-spirost-5-en-3beta-ol / Diosgenin

-
Macromolecule #4: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-...

MacromoleculeName: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
type: ligand / ID: 4 / Number of copies: 4 / Formula: YUY
Molecular weightTheoretical: 841.033 Da
Chemical component information

ChemComp-YUY:
(2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 49.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Number images used: 84000

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7mbp:
Cryo-EM structure of zebrafish TRPM5 in the presence of 1 mM EDTA

+
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