[English] 日本語
Yorodumi
- EMDB-0869: Cryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0869
TitleCryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions
Map data
Sample
  • Complex: MgtE-Fab complex
    • Protein or peptide: Magnesium transporter MgtE
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
Function / homology
Function and homology information


magnesium ion transport / magnesium ion transmembrane transporter activity / magnesium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
MgtE, N-terminal domain superfamily / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / Magnesium transporter MgtE / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. ...MgtE, N-terminal domain superfamily / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / Magnesium transporter MgtE / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Magnesium transporter MgtE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria) / Thermus thermophilus HB8 (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHattori M / Jin F
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: PLoS Biol / Year: 2021
Title: The structure of MgtE in the absence of magnesium provides new insights into channel gating.
Authors: Fei Jin / Minxuan Sun / Takashi Fujii / Yurika Yamada / Jin Wang / Andrés D Maturana / Miki Wada / Shichen Su / Jinbiao Ma / Hironori Takeda / Tsukasa Kusakizako / Atsuhiro Tomita / Yoshiko ...Authors: Fei Jin / Minxuan Sun / Takashi Fujii / Yurika Yamada / Jin Wang / Andrés D Maturana / Miki Wada / Shichen Su / Jinbiao Ma / Hironori Takeda / Tsukasa Kusakizako / Atsuhiro Tomita / Yoshiko Nakada-Nakura / Kehong Liu / Tomoko Uemura / Yayoi Nomura / Norimichi Nomura / Koichi Ito / Osamu Nureki / Keiichi Namba / So Iwata / Ye Yu / Motoyuki Hattori /
Abstract: MgtE is a Mg2+ channel conserved in organisms ranging from prokaryotes to eukaryotes, including humans, and plays an important role in Mg2+ homeostasis. The previously determined MgtE structures in ...MgtE is a Mg2+ channel conserved in organisms ranging from prokaryotes to eukaryotes, including humans, and plays an important role in Mg2+ homeostasis. The previously determined MgtE structures in the Mg2+-bound, closed-state, and structure-based functional analyses of MgtE revealed that the binding of Mg2+ ions to the MgtE cytoplasmic domain induces channel inactivation to maintain Mg2+ homeostasis. There are no structures of the transmembrane (TM) domain for MgtE in Mg2+-free conditions, and the pore-opening mechanism has thus remained unclear. Here, we determined the cryo-electron microscopy (cryo-EM) structure of the MgtE-Fab complex in the absence of Mg2+ ions. The Mg2+-free MgtE TM domain structure and its comparison with the Mg2+-bound, closed-state structure, together with functional analyses, showed the Mg2+-dependent pore opening of MgtE on the cytoplasmic side and revealed the kink motions of the TM2 and TM5 helices at the glycine residues, which are important for channel activity. Overall, our work provides structure-based mechanistic insights into the channel gating of MgtE.
History
DepositionNov 14, 2019-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

-
Structure visualization

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

emd_0869.png

Downloads & links

-
Map

FileDownload / File: emd_0869.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.018
Minimum - Maximum-0.07721349 - 0.12309506
Average (Standard dev.)0.00025640687 (±0.0030026839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z209.920209.920209.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0770.1230.000

-
Supplemental data

-
Sample components

-
Entire : MgtE-Fab complex

EntireName: MgtE-Fab complex
Components
  • Complex: MgtE-Fab complex
    • Protein or peptide: Magnesium transporter MgtE
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain

-
Supramolecule #1: MgtE-Fab complex

SupramoleculeName: MgtE-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Magnesium transporter MgtE

MacromoleculeName: Magnesium transporter MgtE / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 19.249996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LVYSEAGPVA LWLARVRWLV ILILTGMVTS SILQGFESVL EAVTALAFYV PVLLGTGGNT GNQSATLIIR ALATRDLDLR DWRRVFLKE MGVGLLLGLT LSFLLVGKVY WDGHPLLLPV VGVSLVLIVF FANLVGAMLP FLLRRLGVDP ALVSNPLVAT L SDVTGLLI YLSVARLLLE

-
Macromolecule #2: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.837455 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DVLMTQTPLS LPVSLGDQAS ISCRSSQSLV HSDGNTYLHW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYFCSQSTHV PWTFGGGTKL EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DVLMTQTPLS LPVSLGDQAS ISCRSSQSLV HSDGNTYLHW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYFCSQSTHV PWTFGGGTKL EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNR

-
Macromolecule #3: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.092789 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVKLQESGVE LVKPGASVKI SCKASGYSFT GYNMNWVKQS HGKSLEWIGN ISPYYGTSIY NQNFKGKATL TVDRSSSTAY MQLNSLTSE DSAVYYCARG ESFSNYEGYY AMDYWGQGTS VIVSSAKTTA PSVYPLAPVC GDTSGSSVTL GCLVKGYFPE P VTLTWNSG ...String:
EVKLQESGVE LVKPGASVKI SCKASGYSFT GYNMNWVKQS HGKSLEWIGN ISPYYGTSIY NQNFKGKATL TVDRSSSTAY MQLNSLTSE DSAVYYCARG ESFSNYEGYY AMDYWGQGTS VIVSSAKTTA PSVYPLAPVC GDTSGSSVTL GCLVKGYFPE P VTLTWNSG SLSSGVHTFP AVLQSDLYTL SSSVTVTSST WPSQSITCNV AHPASSTKVD KKIEPR

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168911
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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