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- PDB-7qru: Structure of Bacillus pseudofirmus Mrp antiporter complex, monomer -

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Basic information

Entry
Database: PDB / ID: 7qru
TitleStructure of Bacillus pseudofirmus Mrp antiporter complex, monomer
Components
  • (Na(+)/H(+) antiporter subunit ...) x 3
  • (Na+/H+ antiporter subunit ...) x 4
KeywordsMEMBRANE PROTEIN / Antiporter / Electron transport / Complex
Function / homology
Function and homology information


: / monoatomic ion transmembrane transporter activity / monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / antiporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / membrane => GO:0016020 / ATP synthesis coupled electron transport / monoatomic ion transport ...: / monoatomic ion transmembrane transporter activity / monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / antiporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / membrane => GO:0016020 / ATP synthesis coupled electron transport / monoatomic ion transport / proton transmembrane transport / plasma membrane
Similarity search - Function
Monovalent cation proton antiporter subunit A / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / : / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter ...Monovalent cation proton antiporter subunit A / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / : / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter / Multiple resistance and pH regulation protein F (MrpF / PhaF) / MBH, subunit D / Helix Hairpins - #3510 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Na+/H+ antiporter subunit D / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G1 / Na(+)/H(+) antiporter subunit B / Na+/H+ antiporter subunit A / Na(+)/H(+) antiporter subunit F / Na(+)/H(+) antiporter subunit C
Similarity search - Component
Biological speciesAlkalihalophilus pseudofirmus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsLee, Y.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/5-1 Germany
CitationJournal: 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
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Na+/H+ antiporter subunit D
A: Na+/H+ antiporter subunit A
B: Na(+)/H(+) antiporter subunit B
C: Na(+)/H(+) antiporter subunit C
E: Na+/H+ antiporter subunit E
F: Na(+)/H(+) antiporter subunit F
G: Na+/H+ antiporter subunit G1
e: Na+/H+ antiporter subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,81711
Polymers233,5738
Non-polymers2,2443
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Na+/H+ antiporter subunit ... , 4 types, 5 molecules DAEeG

#1: Protein Na+/H+ antiporter subunit D


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
#2: Protein Na+/H+ antiporter subunit A


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 Na+/H+ antiporter subunit E


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 Na+/H+ antiporter subunit G1


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

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Na(+)/H(+) antiporter subunit ... , 3 types, 3 molecules BCF

#3: Protein Na(+)/H(+) antiporter subunit B


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
#4: Protein Na(+)/H(+) antiporter subunit C / Mrp complex subunit C / Multiple resistance and pH homeostasis protein C


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 Na(+)/H(+) antiporter subunit F


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

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Non-polymers , 2 types, 363 molecules

#8: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: MrpABCDEFG complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Alkalihalobacillus pseudofirmus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 513743 / Symmetry type: POINT

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