[English] 日本語
Yorodumi
- EMDB-6975: 3.3 angstrom structure of mouse TRPM7 with EDTA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6975
Title3.3 angstrom structure of mouse TRPM7 with EDTA
Map data
Sample
  • Cell: Membrane Protein, Transient Receptor Potential ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 7
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsCryoEM / Truncated mouse TRPM7 / MEMBRANE PROTEIN / TRANSFERASE
Function / homology
Function and homology information


intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / monoatomic cation transmembrane transport / necroptotic process / monoatomic cation channel activity / ruffle ...intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / monoatomic cation transmembrane transport / necroptotic process / monoatomic cation channel activity / ruffle / protein tetramerization / calcium channel activity / memory / synaptic vesicle membrane / calcium ion transport / kinase activity / actin binding / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily M member 7 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / SLOG in TRPM ...Transient receptor potential cation channel subfamily M member 7 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / SLOG in TRPM / Ion transport domain / Ion transport protein / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZhang J / Li Z
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure of the mammalian TRPM7, a magnesium channel required during embryonic development.
Authors: Jingjing Duan / Zongli Li / Jian Li / Raymond E Hulse / Ana Santa-Cruz / William C Valinsky / Sunday A Abiria / Grigory Krapivinsky / Jin Zhang / David E Clapham /
Abstract: The transient receptor potential ion channel subfamily M, member 7 (TRPM7), is a ubiquitously expressed protein that is required for mouse embryonic development. TRPM7 contains both an ion channel ...The transient receptor potential ion channel subfamily M, member 7 (TRPM7), is a ubiquitously expressed protein that is required for mouse embryonic development. TRPM7 contains both an ion channel and an α-kinase. The channel domain comprises a nonselective cation channel with notable permeability to Mg and Zn Here, we report the closed state structures of the mouse TRPM7 channel domain in three different ionic conditions to overall resolutions of 3.3, 3.7, and 4.1 Å. The structures reveal key residues for an ion binding site in the selectivity filter, with proposed partially hydrated Mg ions occupying the center of the conduction pore. In high [Mg], a prominent external disulfide bond is found in the pore helix, which is essential for ion channel function. Our results provide a structural framework for understanding the TRPM1/3/6/7 subfamily and extend the knowledge base upon which to study the diversity and evolution of TRP channels.
History
DepositionMay 18, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5zx5
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6975.png

Downloads & links

-
Map

FileDownload / File: emd_6975.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.05
Minimum - Maximum-0.20629883 - 0.37686768
Average (Standard dev.)0.0005016515 (±0.009046897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2060.3770.001

-
Supplemental data

-
Sample components

-
Entire : Membrane Protein, Transient Receptor Potential ion channel

EntireName: Membrane Protein, Transient Receptor Potential ion channel
Components
  • Cell: Membrane Protein, Transient Receptor Potential ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 7
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: Membrane Protein, Transient Receptor Potential ion channel

SupramoleculeName: Membrane Protein, Transient Receptor Potential ion channel
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Transient receptor potential cation channel subfamily M member 7

MacromoleculeName: Transient receptor potential cation channel subfamily M member 7
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 141.417719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SQKSWIESTL TKRECVYIIP SSKDPHRCLP GCQICQQLVR CFCGRLVKQH ACFTASLAMK YSDVKLGEHF NQAIEEWSVE KHTEQSPTD AYGVINFQGG SHSYRAKYVR LSYDTKPEII LQLLLKEWQM ELPKLVISVH GGMQKFELHP RIKQLLGKGL I KAAVTTGA ...String:
SQKSWIESTL TKRECVYIIP SSKDPHRCLP GCQICQQLVR CFCGRLVKQH ACFTASLAMK YSDVKLGEHF NQAIEEWSVE KHTEQSPTD AYGVINFQGG SHSYRAKYVR LSYDTKPEII LQLLLKEWQM ELPKLVISVH GGMQKFELHP RIKQLLGKGL I KAAVTTGA WILTGGVNTG VAKHVGDALK EHASRSSRKI CTIGIAPWGV IENRNDLVGR DVVAPYQTLL NPLSKLNVLN NL HSHFILV DDGTVGKYGA EVRLRRELEK TINQQRIHAR IGQGVPVVAL IFEGGPNVIL TVLEYLQESP PVPVVVCEGT GRA ADLLAY IHKQTEEGGN LPDAAEPDII STIKKTFNFG QSEAVHLFQT MMECMKKKEL ITVFHIGSED HQDIDVAILT ALLK GTNAS AFDQLILTLA WDRVDIAKNH VFVYGQQWLV GSLEQAMLDA LVMDRVSFVK LLIENGVSMH KFLTIPRLEE LYNTK QGPT NPMLFHLIRD VKQGNLPPGY KITLIDIGLV IEYLMGGTYR CTYTRKRFRL IYNSLGGNNR RSGRNTSSST PQLRKS HET FGNRADKKEK MRHNHFIKTA QPYRPKMDAS MEEGKKKRTK DEIVDIDDPE TKRFPYPLNE LLIWACLMKR QVMARFL WQ HGEESMAKAL VACKIYRSMA YEAKQSDLVD DTSEELKQYS NDFGQLAVEL LEQSFRQDET MAMKLLTYEL KNWSNSTC L KLAVSSRLRP FVAHTCTQML LSDMWMGRLN MRKNSWYKVI LSILVPPAIL MLEYKTKAEM SHIPQSQDAH QMTMEDSEN NFHNITEEIP MEVFKEVKIL DSSDGKNEME IHIKSKKLPI TRKFYAFYHA PIVKFWFNTL AYLGFLMLYT FVVLVKMEQL PSVQEWIVI AYIFTYAIEK VREVFMSEAG KISQKIKVWF SDYFNVSDTI AIISFFVGFG LRFGAKWNYI NAYDNHVFVA G RLIYCLNI IFWYVRLLDF LAVNQQAGPY VMMIGKMVAN MFYIVVIMAL VLLSFGVPRK AILYPHEEPS WSLAKDIVFH PY WMIFGEV YAYEIDVCAN DSTLPTICGP GTWLTPFLQA VYLFVQYIIM VNLLIAFFNN VYLQVKAISN IVWKYQRYHF IMA YHEKPV LPPPLIILSH IVSLFCCVCK RRKKDKTSDG PKLFLTEEDQ KKLHDFEEQC VEMYFDEKDD KFNSGSEERI RVTF ERVEQ MSIQIKEVGD RVNYIKRSLQ SLDS

UniProtKB: Transient receptor potential cation channel subfamily M member 7

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

DetailsTRPM7 image stacks were recorded on Gatan K2 Summit (Gatan) direct detector set in super-resolution counting mode using SerialEM
Particle selectionNumber selected: 2068004
Details: Particle picking and subsequent bad particle elimination through 2D classification was performed using Python scripts/programs developed by Maofu Liao (Ru et al., 2015) with minor ...Details: Particle picking and subsequent bad particle elimination through 2D classification was performed using Python scripts/programs developed by Maofu Liao (Ru et al., 2015) with minor modifications in the 8x binned images.
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1039775
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: RANDOM ASSIGNMENT
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://pdbjlvh1.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