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- PDB-6z16: Structure of the Mrp antiporter complex -

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Basic information

Entry
Database: PDB / ID: 6z16
TitleStructure of the Mrp antiporter complex
Components(Multisubunit Na+/H+ antiporter, ...) x 7
KeywordsMEMBRANE PROTEIN / Mrp antiporter / sodium/proton exchanger / bioenergetics / complex
Function / homology
Function and homology information


sodium:proton antiporter activity / monoatomic cation transmembrane transporter activity / antiporter activity / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / monoatomic ion transport / proton transmembrane transport / membrane / plasma membrane
Similarity search - Function
Monovalent cation proton antiporter subunit A / : / : / MrpA C-terminal/MbhE / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like ...Monovalent cation proton antiporter subunit A / : / : / MrpA C-terminal/MbhE / : / MBH, subunit E / 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 / 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 / Proton-conducting membrane transporter
Similarity search - Domain/homology
: / PHOSPHATIDYLETHANOLAMINE / Multisubunit Na+/H+ antiporter, G subunit / Multisubunit Na+/H+ antiporter, C subunit / Multisubunit Na+/H+ antiporter, B subunit / Multisubunit Na+/H+ antiporter, A subunit / Multisubunit Na+/H+ antiporter, F subunit / Multisubunit Na+/H+ antiporter, E subunit / Multisubunit Na+/H+ antiporter, D subunit
Similarity search - Component
Biological speciesAnoxybacillus flavithermus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsSteiner, J. / Sazanov, L.A.
CitationJournal: Elife / Year: 2020
Title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter.
Authors: Julia Steiner / Leonid Sazanov /
Abstract: Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na (or K)/H exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. ...Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na (or K)/H exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.
History
DepositionMay 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Multisubunit Na+/H+ antiporter, A subunit
B: Multisubunit Na+/H+ antiporter, B subunit
C: Multisubunit Na+/H+ antiporter, C subunit
D: Multisubunit Na+/H+ antiporter, D subunit
E: Multisubunit Na+/H+ antiporter, E subunit
F: Multisubunit Na+/H+ antiporter, F subunit
G: Multisubunit Na+/H+ antiporter, G subunit
a: Multisubunit Na+/H+ antiporter, A subunit
b: Multisubunit Na+/H+ antiporter, B subunit
c: Multisubunit Na+/H+ antiporter, C subunit
d: Multisubunit Na+/H+ antiporter, D subunit
e: Multisubunit Na+/H+ antiporter, E subunit
f: Multisubunit Na+/H+ antiporter, F subunit
g: Multisubunit Na+/H+ antiporter, G subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,18344
Polymers426,94114
Non-polymers19,24130
Water00
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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Multisubunit Na+/H+ antiporter, ... , 7 types, 14 molecules AaBbCcDdEeFfGg

#1: Protein Multisubunit Na+/H+ antiporter, A subunit


Mass: 92059.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpA, Aflv_1952 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GL84
#2: Protein Multisubunit Na+/H+ antiporter, B subunit


Mass: 15421.317 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpB, Aflv_1951 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GL83
#3: Protein Multisubunit Na+/H+ antiporter, C subunit


Mass: 11625.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpC, Aflv_1950 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GL82
#4: Protein Multisubunit Na+/H+ antiporter, D subunit


Mass: 53767.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpD, Aflv_1949 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GL98
#5: Protein Multisubunit Na+/H+ antiporter, E subunit


Mass: 18037.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpE, Aflv_1948 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GL97
#6: Protein Multisubunit Na+/H+ antiporter, F subunit


Mass: 9657.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpF, Aflv_1947 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GL96
#7: Protein Multisubunit Na+/H+ antiporter, G subunit


Mass: 12900.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus flavithermus (strain DSM 21510 / WK1) (bacteria)
Gene: mrpG, Aflv_1946 / Plasmid: pET Duet-1 / Cell line (production host): KNabc / Production host: Escherichia coli (E. coli) / References: UniProt: B7GIG3

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Non-polymers , 2 types, 30 molecules

#8: Chemical...
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#9: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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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: Mrp dimer / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.44 MDa / Experimental value: NO
Source (natural)Organism: Anoxybacillus flavithermus WK1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: KNabc
Buffer solutionpH: 6
SpecimenConc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 88 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIX1.12-2829model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 892069
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285688 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14HEA

4hea

14HEA1PDBexperimental model
26CFW

6cfw

16CFW2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00830962
ELECTRON MICROSCOPYf_angle_d1.05941942
ELECTRON MICROSCOPYf_dihedral_angle_d8.13318132
ELECTRON MICROSCOPYf_chiral_restr0.1715014
ELECTRON MICROSCOPYf_plane_restr0.0094948

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