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Yorodumi- PDB-7qru: Structure of Bacillus pseudofirmus Mrp antiporter complex, monomer -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qru | ||||||
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Title | Structure of Bacillus pseudofirmus Mrp antiporter complex, monomer | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Antiporter / Electron transport / Complex | ||||||
Function / homology | Function and homology information : / monoatomic ion transmembrane transporter activity / inorganic cation transmembrane transport / monoatomic cation transmembrane transporter activity / antiporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / membrane => GO:0016020 / monoatomic ion transport ...: / monoatomic ion transmembrane transporter activity / inorganic cation transmembrane transport / monoatomic cation transmembrane transporter activity / antiporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / membrane => GO:0016020 / monoatomic ion transport / proton transmembrane transport / plasma membrane Similarity search - Function | ||||||
Biological species | Alkalihalophilus pseudofirmus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å | ||||||
Authors | Lee, Y. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations. Authors: Yongchan Lee / Outi Haapanen / Anton Altmeyer / Werner Kühlbrandt / Vivek Sharma / Volker Zickermann / Abstract: Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are ...Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ~70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated trans-membrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qru.cif.gz | 405.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qru.ent.gz | 325.4 KB | Display | PDB format |
PDBx/mmJSON format | 7qru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qru_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7qru_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7qru_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 7qru_validation.cif.gz | 104.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/7qru ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qru | HTTPS FTP |
-Related structure data
Related structure data | 14124MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Na+/H+ antiporter subunit ... , 4 types, 5 molecules DAEeG
#1: Protein | Mass: 54605.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Gene: BTR22_14495 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PMS5 | ||
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#2: Protein | Mass: 89301.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Gene: BTR22_14510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PN15 | ||
#5: Protein | Mass: 18357.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Gene: BTR22_14490 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PMT4 #7: Protein | | Mass: 14947.675 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Gene: BTR22_14480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PMU8 |
-Na(+)/H(+) antiporter subunit ... , 3 types, 3 molecules BCF
#3: Protein | Mass: 15748.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Gene: BTR22_14505 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PN06 |
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#4: Protein | Mass: 12229.499 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Strain: ATCC BAA-2126 / JCM 17055 / OF4 / Gene: mrpC, BpOF4_13200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RGZ3 |
#6: Protein | Mass: 10024.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalophilus pseudofirmus (bacteria) Gene: BTR22_14485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PNA0 |
-Non-polymers , 2 types, 363 molecules
#8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: MrpABCDEFG complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Alkalihalobacillus pseudofirmus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 513743 / Symmetry type: POINT |