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- PDB-6lbh: Cryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions -

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Basic information

Entry
Database: PDB / ID: 6lbh
TitleCryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions
Components
  • Fab heavy chain
  • Fab light chain
  • Magnesium transporter MgtE
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / channel / 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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Magnesium transporter MgtE
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHattori, M. / Jin, F.
Funding support China, 1items
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Magnesium transporter MgtE
B: Magnesium transporter MgtE
D: Fab light chain
C: Fab heavy chain
F: Fab light chain
E: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)134,3606
Polymers134,3606
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16430 Å2
ΔGint-97 kcal/mol
Surface area49240 Å2

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Components

#1: Protein Magnesium transporter MgtE


Mass: 19249.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SMG8
#2: Antibody Fab light chain


Mass: 23837.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab heavy chain


Mass: 24092.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MgtE-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168911 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069435
ELECTRON MICROSCOPYf_angle_d0.79512908
ELECTRON MICROSCOPYf_dihedral_angle_d17.3731322
ELECTRON MICROSCOPYf_chiral_restr0.0461539
ELECTRON MICROSCOPYf_plane_restr0.0051612

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