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- EMDB-0869: Structure of a membrane protein -

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Basic information

Entry
Database: EMDB / ID: EMD-0869
TitleStructure of a membrane protein
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
Keywordschannel / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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

emd_0869.png

Downloads & links

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Map

FileDownload / File: emd_0869.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Sample components

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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

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Supramolecule #1: MgtE-Fab complex

SupramoleculeName: MgtE-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus (bacteria)

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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

UniProtKB: Magnesium transporter MgtE

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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

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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

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: NONE
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)

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