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Yorodumi- PDB-6lbh: Cryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lbh | ||||||
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Title | Cryo-EM structure of the MgtE Mg2+ channel under Mg2+-free conditions | ||||||
Components |
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Keywords | TRANSPORT 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 | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Hattori, M. / Jin, F. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lbh.cif.gz | 209.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lbh.ent.gz | 172.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lbh_validation.pdf.gz | 738 KB | Display | wwPDB validaton report |
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Full document | 6lbh_full_validation.pdf.gz | 764.3 KB | Display | |
Data in XML | 6lbh_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 6lbh_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/6lbh ftp://data.pdbj.org/pub/pdb/validation_reports/lb/6lbh | HTTPS FTP |
-Related structure data
Related structure data | 0869MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 | 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 | 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) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MgtE-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Thermus thermophilus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168911 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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